Housekeeping and tissue-specific genes in mouse tissues

  • Kouame E Kouadjo1,

    Affiliated with

    • Yuichiro Nishida1,

      Affiliated with

      • Jean F Cadrin-Girard1,

        Affiliated with

        • Mayumi Yoshioka1 and

          Affiliated with

          • Jonny St-Amand1Email author

            Affiliated with

            BMC Genomics20078:127

            DOI: 10.1186/1471-2164-8-127

            Received: 20 October 2006

            Accepted: 22 May 2007

            Published: 22 May 2007

            Abstract

            Background

            This study aims to characterize the housekeeping and tissue-specific genes in 15 mouse tissues by using the serial analysis of gene expression (SAGE) strategy which indicates the relative level of expression for each transcript matched to the tag.

            Results

            Here, we identified constantly expressed housekeeping genes, such as eukaryotic translation elongation factor 2, which is expressed in all tissues without significant difference in expression levels. Moreover, most of these genes were not regulated by experimental conditions such as steroid hormones, adrenalectomy and gonadectomy. In addition, we report previously postulated housekeeping genes such as peptidyl-prolyl cis-trans isomerase A, glyceraldehyde-3-phosphate dehydrogenase and beta-actin, which are expressed in all the tissues, but with significant difference in their expression levels. We have also identified genes uniquely detected in each of the 15 tissues and other tissues from public databases.

            Conclusion

            These identified housekeeping genes could represent appropriate controls for RT-PCR and northern blot when comparing the expression levels of genes in several tissues. The results reveal several tissue-specific genes highly expressed in testis and pituitary gland. Furthermore, the main function of tissue-specific genes expressed in liver, lung and bone is the cell defence, whereas several keratins involved in cell structure function are exclusively detected in skin and vagina. The results from this study can be used for example to target a tissue for agent delivering by using the promoter of tissue-specific genes. Moreover, this study could be used as basis for further researches on physiology and pathology of these tissues.

            Background

            Housekeeping genes are constitutively expressed in all tissues to maintain cellular functions [1]. Moreover, they are presumed to produce the minimally essential transcripts necessary for normal cellular physiology [2]. In the validation of GeneChips using real-time RT-PCR, a standard curve of a reference housekeeping gene is thus sufficient for the quantification of multiple genes in a tissue. This is especially advantageous for the validation of GeneChip results because multiple genes are quantified in one tissue sample [3]. However, the expression level of the housekeeping genes may vary among tissues or cells and may change under certain circumstances. On the other hand, the highly specific tissue expression of a gene indicates that the gene performs a tissue-specific function. A feature of housekeeping genes is that, in comparison to tissue-specific genes, they evolve on average more slowly [4]. In addition, the methylation is one of the major epigenetic modifications of DNA in mammalian cells, regulating tissue-specific genes as well a housekeeping genes [5]. Furthermore, the differences in the chromatin features between specific genes and housekeeping genes indicate the involvement of chromatin organisation in the control of gene expression [6]. In addition, despite the most fundamental characteristics of housekeeping genes and specific genes, no previous study has quantified the expression level of the housekeeping genes and the tissue-specific genes in a variety of tissues. Using serial analysis of gene expression (SAGE) strategy which indicates the relative level of expression of each transcript matched to a tag, this study represents, to our knowledge, the first characterization of the tissue-specific genes and housekeeping genes in an extensive array of tissues and organs. Using SAGE method, previous studies have characterized the transcriptome of numerous tissues such as uterus [7], adipose tissue [8, 9], skeletal muscle [10], hypothalamus, cerebral cortex and pituitary gland [11, 12].

            The invention and application of SAGE method have paralleled those of microarray/chip technologies. Whereas hybridization-based technologies may allow for shorter detection times and high throughput expression analysis, the SAGE method not only identifies unknown genes but also quantifies the gene expression level relatively to the total mRNA population. Indeed, the SAGE method can be performed to accurately measure the abundance of both known and novel transcripts on global scale [13]. This method is ideal to analyze a large number of transcripts in a given tissue, and it allows the quantitative cataloguing and comparison of expressed genes under various physiological and pathological states [1315].

            Results

            Number of tags and tag species analyzed

            A total count of 1,834,621 SAGE tags were analyzed for the 15 tissues representing 320,624 tag species. For each tissue, approximately 130,000 tags were sequenced, except for testis, ovary, mammary gland, vagina and bone which had approximately 50,000 tags.

            This study has identified 1,111 ubiquitously expressed transcripts. These genes are expressed in all the tissues and therefore are likely candidates as the genes responsible for cellular maintenance also known as housekeeping genes. Among the ubiquitous genes identified, 280 genes are constantly expressed in all tissues. The rest (831 transcripts) are not expressed at the same level in all the 15 tissues. The 280 transcripts are detected at similar level in each of the 15 tissues and can be useful as a set of controls. In the Table 1, we present the expressions levels of the top 10 constantly expressed housekeeping genes, which are expressed in all tissues without significant difference in expression levels and the previously postulated housekeeping genes. To see if the ratio of the housekeeping genes changes in another condition, we have performed biologically relevant experiments. The data presented in the Table 1 have shown that most of these housekeeping genes are not only constant between intact tissues, but also between tissues that have been subjected to hormones such as dihydrotestosterone (DHT) and glucocorticoid (Gcc), as well as gonadectomy (GDX) and adrenalectomy (ADX) conditions. We have investigated the effects of GDX and DHT in prostate, mammary gland, uterus, vagina, adipose tissue and skeletal muscle as well as the regulation of ADX and Gcc in lung, hypothalamus and pituitary gland. Only ribosomal protein L37 and leukocyte receptor cluster (LRC) member 8 were regulated by GDX compared to the intact mice in mammary gland and prostate, respectively. On the other hand, only the expression level of glyceraldehyde-3-phosphate dehydrogenase (GAPDH), a previously postulated housekeeping gene, was regulated by DHT in adipose tissue and uterus compared to GDX mice. Remarkably, eukaryotic translation elongation factor 2 (eEF-2) was highly and constantly expressed in all the investigated tissues. Despites their moderate levels of expression, proteasome (prosome, macropain) 26 subunit non-ATPase 4, eukaryotic initiation factor 3 (eIF3), and ribosomal protein L38 are constantly expressed in all the tissues. We have also identified three RIKEN cDNAs constantly expressed in all the tissues. The results have also shown that, the previously postulated housekeeping genes namely peptidyl-prolyl cis-trans isomerase A (PPIase), GAPDH, beta-actin are not constantly expressed in all the tissues.
            Table 1

            Housekeeping genes expressed in 15 tissues

                 

            Tissues (total tags count sequenced)

                      

            Tag

            Testis (56909)

            Prostate (143559)

            O vary (56154)

            Mammary gland (40546)

            Uterus (178824)

            Vagina (50819)

            Skin (161093)

            Liver (170384)

            Adipose tissue (158218)

            Lung (159843)

            Bone (74859)

            Skeletal muscle (135530)

            Cerebral cortex (161221)

            Hypothalamus (165981)

            Pituitary gland (128480)

            Regulation by GDX, DHT, ADX or Gcc

            Description [UniGene cluster, GenBank Accession no.]

            General function

            Housekeeping genes constantly expressed

            GCCAAGTGGAG

            109

            87

            216

            94

            141

            203

            147

            154

            184

            159

            123

            146

            96

            129

            111

             

            eukaryotic translation elongation factor 2 [Mm.334671, BB705125]

            Protein synthesis

            GATTCCGTGAG

            79

            85

            186

            92

            128

            191

            161

            81

            106

            127

            126

            85

            98

            147

            88

            GDXm

            ribosomal protein L37 [Mm.10474, AK012544]

            Protein synthesis

            CCTCGGAAAAT

            9

            10

            21

            10

            21

            32

            19

            11

            22

            12

            25

            35

            20

            25

            28

             

            ribosomal protein L38 [Mm.238817, BC055346]

            Protein synthesis

            GTAGCTCACAA

            19

            15

            27

            17

            22

            20

            14

            17

            16

            24

            25

            13

            12

            17

            28

             

            hypothetical protein [Mm.302962, BB767941]

            Protein secretion

            TAACTGGAGGA

            30

            10

            27

            10

            10

            28

            19

            10

            16

            28

            15

            7

            22

            28

            12

            GDXp

            leukocyte receptor cluster (LR C) member 8 [Mm.22831, BC066768]

            Cell defence

            GTGGTGCACAC

            19

            10

            11

            10

            9

            24

            11

            16

            14

            18

            15

            13

            15

            29

            24

             

            RIKEN cDNA C030036P15 gene [Mm.36291, NM_172757]

            Protein binding

            CTCAACAGCAA

            5

            9

            27

            15

            12

            20

            17

            14

            17

            14

            16

            14

            16

            10

            15

             

            eukaryotic translation initiation factor 3, subunit 5 (epsilon) [Mm.182962, NM_025344]

            Protein synthesis

            GGTGATGAGGA

            4

            9

            7

            15

            9

            22

            13

            12

            25

            11

            15

            24

            10

            19

            10

             

            RIKEN cDNA 1500016L11 gene [Mm.295670, NM_026885]

            Cell division

            GGGGCTCTGGC

            16

            9

            20

            10

            10

            12

            10

            16

            16

            8

            25

            21

            8

            7

            6

             

            proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Mm.2261, NM_008951]

            Cell defence

            GCCTCAGAGAC

            7

            5

            9

            10

            10

            14

            9

            5

            13

            14

            7

            11

            18

            19

            13

             

            RIKEN cDNA 2410104I19 gene [Mm.29965, NM_133691]

            translational initiation regulation

            Previously postulated housekeeping genes

            GAGCGTTTTGG

            63

            49

            130a

            84

            119a

            177a

            127a

            54

            296a

            153a

            178a

            93

            238a

            226a

            61

             

            peptidyl-prolyl cis-trans isomerase A (PPIase) [Mm.342899, XM_122578]

            Protein synthesis

            GCCTCCAAGGA

            16

            47a

            98a

            114a

            70a

            175a

            149a

            159a

            366a

            64a

            159a

            2332a

            309a

            267a

            97a

            DHTat, u

            glyceraldehyde-3-phosphate dehydrogenase [Mm.303486, XM_285250]

            Sugar metabolism

            GATACTTGGAA

            28a

            90a

            130a

            171a

            179a

            132a

            107a

            79a

            144a

            295a

            296a

            8

            102a

            86a

            62a

             

            actin, beta, cytoplasmic [Mm.297, BB836462]

            Cell structure

            CCCTGAGTCCA

            52a

            18

            159a

            163a

            102a

            168a

            174a

            88a

            134a

            268a

            444a

            30

            100a

            86a

            31

             

            actin, beta, cytoplasmic [Mm.297, NM_007393]

            Cell structure

            aSignificant difference vs.no.of tags shown in bold (p < 0,05). The tag numbers were normalized by 100000.

            Abbreviation: GDX, gonadectomy; DHT, dihydrotestosterone; ADX, adrenalectomy; Gcc, glucocorticoids;m, mammary gland; p, prostate; at, adipose tissue; u,uterus

            Most expressed tissue-specific genes in the 15 tissues

            We have also identified the genes uniquely detected in each of the 15 tissues. These genes are critical for the specific functions that characterize and distinguish the testis, prostate, ovary, mammary gland, uterus, vagina, skin, liver, adipose tissue, lung, bone, skeletal muscle, cerebral cortex, hypothalamus, and pituitary gland. The specific genes are expressed in only one tissue. Table 2 presents the transcripts exclusively detected in the male sexual organs. Obviously, the levels of gene expression in these tissues were statistically different from the other tissues. The current study shows 61 tissue-specific transcripts in the testis. Despite their moderate expression in the testis, some transcripts such as dipeptidase 3, ankyrin repeat domain 5, and ubiquitin-conjugating enzyme E2N are exclusively found in the testis. In contrast, only 7 transcripts are detected in the prostate as specific genes. Noteworthy, seminal vesicle protein secretion 2 is both highly and exclusively detected in the prostate. According to the transcripts specifically detected in the female sexual organs (Table 3), most of the tissue-specific genes are expressed at lower quantity in the ovary, mammary gland, uterus and vagina in comparison to the majority of specific genes expressed in the male sexual organs. Remarkably, proline-rich acidic protein 1 and the novel transcript with the sequence tag CTGTATTTGGG are both highly and uniquely detected in the uterus and the vagina, respectively. The Table 4 shows the transcripts exclusive to the skin, liver, adipose tissue, lung, bone and skeletal muscle. The majority of tissue-specific genes expressed in the skin are involved in cell structure. Keratin associated protein 8-1 is more expressed than the other tissue-specific genes detected in the skin. We report 26 transcripts exclusively detected in the liver. Moreover, two tissue-specific genes namely albumin 1 and alpha microglobulin/bikunin are also highly expressed in the liver. Despite their low expression in the liver, major urinary protein 1, solute carrier family 27 (fatty acid transporter) member 2 and silica-induced gene 111 are also specifically detected. Furthermore, the tissue-specific transcripts expressed in the lung and the bone are involved in cell defence and we have observed the high expression of the tissue-specific genes such as proteoglycan 2 bone marrow and solute carrier family 4 (anion exchanger) member 1 in the bone. The adipose tissue and the skeletal muscle expressed less tissue-specific genes than the other tissues. Only two transcripts namely leptin and lectin galactose binding soluble 12 are reported as candidate specific genes in the adipose tissue. The transcripts such as myosin light chain phosphorylatable fast skeletal muscle and tropomyosin 3 gamma are both moderately and uniquely detected in the skeletal muscle. Among the brain areas investigated, the pituitary gland expressed more tissue-specific transcripts (Table 5). In addition, the majority of these genes are also highly expressed in this gland. We found 3 genes expressed in cerebral cortex, which were not detected in any of the other 14 tissues. In the hypothalamus, RIKEN cDNA A230109K23 gene is both exclusively and highly detected. To see if the tissue-specific genes were detected in other tissues, we have compared our results to the public data deposited in Gene Expression Omnibus (GEO, NCIBI). The public data have confirmed the exclusive detection of tissue-specific genes in each tissue. The transcripts which were specifically detected in the 15 intact tissues were not expressed in other mouse tissues such as embryonic fibroblasts, heart, thymus, bladder, kidney, spleen and pancreas (Table 2 to 5). In addition, using UniGene and EST expression information in the public databases, the normalized expression (%) of intestine is shown and is compared to our results in Table 2 to 5. All the genes mentioned for the uterus, as well as carbonic anhydrase 1, retinol binding protein 2 cellular and keratin complex 1 acidic gene 13 were also expressed in the intestine tissue.
            Table 2

            Specific genes expressed in the male sexual organs

                            

            Tissues from GEO and accession number

               

            Tag

            Testis

            Prostate

            Ovary

            Mammary gland

            Uterus

            Vagina

            Skin

            Liver

            Adipose tissue

            Lung

            Bone

            Skeletal muscle

            Cerebral cortex

            Hypothalamus

            Pituitary gland

            Mouse embryonic fibroblasts GSM7759

            Heart normal GSM106587

            Thymus normal GSM106587

            Bladder normal GSM106599

            Kidney normal GSM56242

            Spleen normal GSM106591

            Pancreas normal GSM 106592

            Intestine UniGene and EST expression (%)

            Description [UniGene cluster, GenBank Accession No]

            General function

               Testis

                                     

            TCGATGTCTGA

            1221

            0a

            4a

            0a

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            protamine 2 [Mm.325769, NM_008933]

            Cell signaling

            AGGACATCAGA

            601

            0a

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            transition protein 1 [Mm.661, NM_009407]

            Cell signaling

            AAACAGAGTCT

            391

            0a

            2a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            t-complex-associated testis expressed 3 [Mm.272173, NM_011560]

            Cell signaling

            GTGCCAGGAGA

            241

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GGTCTGGCTGG

            234

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            tubulin, alpha 3 [Mm.287784, NM_009446]

            Cell signaling

            GCTCCACTGGT

            227

            0a

            0a

            0a

            0a

            8

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            diazepam binding inhibitor-like 5 [Mm.347413, BC048474]

            Cell signaling

            ACCGCTGAGGA

            222

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            lactate dehydrogenase 3, C chain, sperm specific [Mm.16563, NM_013580]

            Energy metabolism

            TGCAACTGGCC

            201

            0a

            0a

            0a

            1a

            2a

            1a

            0a

            0a

            1a

            1a

            0a

            0a

            2a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0

            outer dense fiber of sperm tails 2 [Mm.330116, NM_013615]

            Cell defence

            TTCCATCTCTG

            190

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            ornithine decarboxylase antizym e 3 [Mm.331200, NM_016901]

            Amoni acid metabolism

            TTTAGCCGAGA

            180

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            glyceraldehyde-3-phosphate dehydrogenase, sperm atogenic [Mm.1729, NM_008085]

            Energy metabolism

            TACACGAGGAT

            178

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            transition protein 2 [Mm.206798, NM_013694]

            Cell signaling

            GCCAGATACCG

            139

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            protamine 1 [Mm.42733, NM_013637]

            Cell signaling

            GATTAAAGCTT

            134

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            transition protein 2 [Mm.206798, NM_013694]

            Cell signaling

            GCGTGCTCAGA

            132

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            RIKEN cDNA 4921511K06 gene [Mm.251303, AK160245]

            Cytokinesis, cell shape, secretion and capping

            TAGCCCCTGCA

            125

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            outer dense fiber of sperm tails 1 [Mm.252830, NM_008757]

            Cell defence

            CCCTTTTTCAA

            123

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            sperm mitochondria-associated cysteine-rich protein [Mm.331192, NM_008574]

            Sperm motility

            CAGGAACACGG

            111

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GTCGACCGATG

            100

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            meiosis expressed gene 1 [Mm.2688, CN833209]

            Potein binding

            CAGCTCAAGTG

            99

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            ATPase, C lass I, type 8B, member 3 [Mm.52511, NM_026094]

            Energy metabolism, transport

            CCAATTGCTAC

            95

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            histone H1-like protein in spermatids 1 [Mm.30482, NM_018792]

            Cell division

            TCGGTGCCTCT

            88

            0a

            2a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            DnaJ (H sp40) homolog, subfamily B, member 3 [Mm.3075, NM_008299]

            Cell defence

            GTGCTGGCTTG

            88

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            ACACCCACGCG

            83

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            sperm atogenic Zip 1 [Mm.23520, NM_030237]

            Transcription factor activity

            AAAAAGACCAA

            81

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            centrin 1 [Mm.195831, NM_007593]

            Cell structure

            AAGGCCTGCCA

            78

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            chaperonin containing TC P1, subunit 4 [Mm.332809, BU962071]

            Cell protein synthesis

            AACAATGTTGT

            72

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            fatty acid binding protein 9, testis [Mm.26654, NM_011598]

            Lipid metabolism

            TTCAGCAACGG

            72

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            t-complex protein 10b [Mm.326683, NM_011553]

            Cell signaling

            TCTCGCAATGG

            63

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            tubby-like protein 2 [Mm.280778, NM_008807]

            Phosphoric diester hydrolase Activity

            CTGGATGGTTT

            60

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            actin-like 7b [Mm.251434, NM_025271]

            Cell structure

            ACCTGCAGCCT

            58

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            heat shock protein, alpha-crystallin-related, B9 [Mm.46175, XM_126494]

            Cell defence

            AACAAAAATCC

            58

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            3

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            testis specific gene A2 [Mm.12743, NM_025290]

            Cell signaling

            CGCGGAATGCT

            56

            0a

            0a

            0a

            1a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            PH D finger protein 7 [Mm.5348, BY099053]

            Protein synthesis

            TCTTGCGGCGG

            55

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            DnaJ (H sp40) homolog, subfamily B, member 3 [Mm.3075, AK005688]

            Cell defence

            GAGCAGGTCCA

            48

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            kinesin family member 2B [Mm.67677, XM_126653]

            Cell structure

            TCTTCTGCCTC

            46

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            serine/threonine kinase 22B (sperm iogenesis associated) [Mm.310201, NM_009436]

            Metabolism: protein modification

            GTGTGCGGACC

            44

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            2a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            sperm associated antigen 4 [Mm.81035, AK028080]

            Cell defence

            AATCCATCCAG

            44

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            thioredoxin domain containing 2 (sperm atozoa) [Mm.255732, NM_153519]

            Cell defence

            GCTCCTTTAAA

            42

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            cytochrome coxidase, subunit VIIIc [Mm.660, XM_354691]

            Energy metabolism

            ACCTAGGCAGA

            42

            0

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            testis specific gene A8 [Mm.143832, AB032764]

            Rhabdomere development and photoreceptor cell survival

            CTAATCAGGAG

            41

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            thioredoxin reductase 1 [Mm.210155, NM_025499]

            Cell defence

            CAAGAGCCTCA

            41

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            selenoprotein W [Mm.212777, NM_175033]

            Cell defence

            TGCCCCAACAT

            41

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            oxysterol binding protein 2 [Mm.348003, BC058602]

            Transport

            CACGAAGTTCC

            39

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            neighbor of Brca1 gene 1 [Mm.784, AF227188]

            Zing and ion binding

            ATAGGATGCTG

            37

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            tudor domain containing 6 [Mm.329058, NM_198418]

            Oogenesis

            GCTTGAAGCCT

            35

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            serine/threonine kinase 22A (sperm iogenesis associated) [Mm.347554, XM_147244]

            Metabolism: protein modification

            GTGCCTACCTA

            33

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            1a

            0a

            0a

            1a

            1a

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            Park2 co-regulated [Mm.18889, XM_128418]

            Sperm differentiation

            TGGGTGAAGGG

            33

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            tripartite motif protein 17 [Mm.179733, NM_031172]

            Ubiquitin-protein ligase activity

            GAAATCTTATG

            33

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            four and a half LIM domains 5 [Mm.87325, NM_021318]

            Transcription

            GACAAGCAGAC

            32

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            1a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            translin-associated factor X (Tsnax) interacting protein 1 [Mm.28323, NM_024445]

            Protein binding

            AGGGTGGACAA

            30

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            DnaJ (H sp40) homolog, subfamily B, member 8 [Mm.272871, NM_019964]

            Cell defence

            GGCTCAATTTC

            30

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            StAR -related lipid transfer (STAR T) domain containing 6 [Mm.83623, BC061022]

            Cell signaling

            TGTTCTTCACT

            30

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            sperm associated antigen 9 [Mm.260737, AK034670]

            Cell defence

            CCCTGGGAGAC

            30

            0a

            2a

            0a

            0a

            0a

            0a

            0a

            1a

            1

            0a

            1a

            1a

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            sterile alpha motif domain containing 4 [Mm.269139, XM_127686]

            Post-transcriptional regulators

            GTCGCTGTCTT

            28

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            fibronectin type 3 and ankyrin repeat domains 1 [Mm.87448, AK017071]

            Transcription factor activity and DNA binding

            CCTTCTGTCGG

            28

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            t-complex protein 10b [Mm.326683, NM_009340]

            Cell signaling

            GCTACGCTCAC

            28

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            dipeptidase 3 [Mm.173395, NM_027960]

            Protein synthesis

            CAGACCAACGC

            28

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            testis specific 10 interacting protein [Mm.329659, AK019010]

            Cell signaling

            ATGCCTTTCCA

            26

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            ankyrin repeat domain 5 [Mm.198389, NM_175667]

            Cell structure

            AACAATATTTA

            26

            0a

            0a

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            ubiquitin-conjugating enzyme E2N [Mm.328239, AK005788]

            Protein synthesis

            GCTGCATAACA

            26

            0a

            0a

            0a

            0a

            0a

            0a

            3

            1a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            aquaporin 11 [Mm.29756, NM_175105]

            Transport

               Prostate

                               

            0a

                 

            ACCCAGACACG

            0a

            193

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            seminal vesicle protein, secretion 2 [Mm.99395, BB872622]

            Protein secretion

            TGACAAAACGT

            0a

            99

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            beta-microseminoprotein [Mm.2540, NM_020597]

            Cell signaling

            AAGACGGGTAG

            0a

            91

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            C U B and zona pellucida-like domains 1 [Mm.304207, BE852974]

            Cell signaling

            GCAACTAGCCT

            0a

            66

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            serine peptidase inhibitor, Kazal type 3 [Mm.272, DV071569]

            Peptidase activity

            GTGAGAAACAC

            0a

            52

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            TATTTTGCAAT

            0a

            49

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            seminal vesicle antigen [Mm.4119, NM_009299]

            Protein secretion

            CCTGGTGAAAG

            0a

            45

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            mucin 10, submandibular gland salivary mucin [Mm.200411, NM_008644]

            Spermatogenesis

            a Significant difference vs. no. of tags show n in bold (p < 0,05)

            Table 3

            Specific genes expressed in the female sexual organs

                            

            Tissues from GEO and accession number

               

            Tag

            Testis

            Prostate

            Ovary

            Mammary gland

            Uterus

            Vagina

            Skin

            Liver

            Adipose tissue

            Lung

            Bone

            Skeletal muscle

            Cerebral cortex

            Hypothalamus

            Pituitary gland

            Mouse embryonic fibroblasts GSM7759

            Heart normal GSM106587

            Thymus normal GSM106596

            Bladder normal GSM106599

            Kidney normal GSM56242

            Spleen normal GSM106591

            Pancreas Normal GSM106592

            Intestine UniGene and EST expression (%)

            Description [UniGene cluster, GenBank Accession No]

            General function

               Ovary

                                     

            TGGCAGAAGCC

            0a

            0a

            73

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            RIKEN cDNA 4930583H14 gene [Mm.273339, NM_026358]

            Protein secretion

            GTCAACACAGG

            2a

            0a

            38

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            CATATGTTGAT

            2a

            0a

            36

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            RIKEN cDNA 4921521F21 gene [Mm.18725, NM_027582]

            catalyzes the reduction of 2,5-diketo-d-gluconic acid

               Mammary gland

                                     

            TCCGGAGAAAA

            0a

            1a

            0a

            35

            0a

            0a

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            CTAGGTGGTGC

            0a

            0a

            0a

            32

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            glycosylation dependent cell adhesion molecule 1 [Mm.219621, NM_008134]

            Cell signaling

               Uterus

                                     

            TCTGACGATGT

            0a

            0a

            0a

            0a

            130

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            73

            proline-rich acidic protein 1 [Mm.141646, NM_009475]

            Cell signaling

            GAAGCTGTATG

            0a

            0a

            2a

            0a

            33

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            2a

            0a

            0a

            25

            Hydroxysteroid 11-beta dehydrogenase 2 [Mm.5079, BC014753]

            Steroid hormone synthesis

            TACATAGATGG

            0a

            1a

            0a

            0a

            31

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            85

            chloride channel calcium activated 3 [Mm.33483, NM_017474]

            Cell signaling

               Vagina

                                     

            CTGTATTTGGG

            0a

            0a

            0a

            0a

            2a

            114

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            AAGCACCAAAT

            0a

            0a

            0a

            0a

            2a

            85

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            AAAGCATCCTT

            0a

            0a

            0a

            0a

            1a

            77

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin intermediate filament 16a [Mm.343031, XM_484082]

            Cell structure

            CAGAACCTCAA

            0a

            0a

            0a

            0a

            1a

            39

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            26

            keratin complex 1, acidic, gene 13 [Mm.4646, BY709670]

            Cell structure

            GCCTTGGAGGT

            0a

            0a

            0a

            0a

            2a

            35

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin complex 2, basic, gene 6 g [Mm.22657, NM_010669]

            Cell structure

            GGGACTCCTCC

            0a

            0a

            0a

            0a

            0a

            34

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            9a

            84

            retinol binding protein 2, cellular [Mm.12825, NM_009034]

            Intracellular transport

            a Significant difference vs. no. of tags show n in bold (p < 0,05)

            Table 4

            Specific genes expressed in the skin, liver, adipose tissue, lungs, bone, and skeletal muscle

                            

            Tissues from GEO and accession number

               

            Tag

            Testis

            Prostate

            Ovary

            Mammary gland

            Uterus

            Vagina

            Skin

            Liver

            Adipose tissue

            Lung

            Bone

            Skeletal muscle

            Cerebral cortex

            Hypothalamus

            Pituitary gland

            Mouse embryonic fibroblasts GSM7759

            Heart normal GSM106587

            Thymus normal GSM106587

            Bladder normal GSM106599

            Kidney normal GSM56242

            Spleen normal GSM106591

            Pancreas normal GSM 106592

            Intestine UniGene and EST expression (%)

            Description [UniGene cluster, GenBank Accession No]

            General function

               Skin

                                     

            ATTCCCTGTTA

            0a

            0a

            0a

            0a

            0a

            0a

            299

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 8-1 [Mm.13979, D86423]

            Cell structure

            AAGTGAAAGCA

            0a

            0a

            0a

            0a

            0a

            0a

            204

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            trichohyalin - human [Mm.1160, CD545918]

            Fibrillar forming collagen

            CCTCCATTTCC

            0a

            0a

            0a

            0a

            0a

            0a

            86

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin complex 1, acidic, gene 4 [Mm.289644, NM_027563]

            Cell structure

            GTTCTCAGTAT

            0a

            0a

            0a

            0a

            0a

            0a

            66

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 6-1 [Mm.310892, D86419]

            Cell structure

            TTGCTTCTGGG

            0a

            0a

            0a

            0a

            0a

            0a

            65

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 3-2 [Mm.46389, NM_025720]

            Cell structure

            AAGCTTTGATA

            0a

            0a

            0a

            0a

            0a

            0a

            59

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 16-5 [Mm.28425, NM_130857]

            Cell structure

            GCTTCACCTTG

            0a

            0a

            0a

            0a

            0a

            0a

            40

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 11-1 [Mm.310906, AV018433]

            Cell structure

            ATGGTCTGAGC

            0a

            0a

            0a

            0a

            0a

            0a

            40

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            S100 calcium binding protein A17 [Mm.68064, NM_027762]

            Cell signaling

            CAACTCCTTTG

            0a

            0a

            0a

            0a

            0a

            0a

            35

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin complex 1, acidic, gene 1 [Mm.19109, NM_010659]

            Cell structure

            GGCCTGGCTTA

            0a

            0a

            0a

            0a

            0a

            0a

            35

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            lymphocyte antigen 6 complex, locus G6C [Mm.215096, NM_023463]

            Cell defence

            GTACTGTCTTG

            0a

            0a

            0a

            0a

            0a

            0a

            34

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            keratin associated protein 4.7 (Homo sapiens) [Mm.340791, AV089658]

            Cell structure

            TCCTGCACAAT

            0a

            0a

            0a

            0a

            0a

            0a

            25

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            G protein-coupled receptor, family C, group 5, member D [Mm.49902, NM_053118]

            Cell signaling

               Liver

                                     

            AAGACTCAGGA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            185

            0a

            0a

            3a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            albumin 1 [Mm.16773, NM_009654]

            Cell defence

            TCGGACCATAG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            120

            1a

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            alpha 1 microglobulin/bikunin [Mm.2197, NM_007443]

            Cell defence

            CAAATAGGTTG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            101

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            serine (or cysteine) proteinase inhibitor, clade A, member 1a [Mm.259233, AI527352]

            Cell defence

            ACCCTTAGAGA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            93

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            betaine-homocysteine methyltransferase [Mm.329582, NM_016668]

            Amino acid metabolism

            GCCACGCCCCC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            89

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            4-hydroxyphenylpyruvic acid dioxygenase [Mm.6584, NM_008277]

            Amino acid metabolism

            GTGATTGCTGA

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            79

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            murinoglobulin 2 [Mm.244937, NM_008646]

            Cell defence

            TGTTCCGTCTG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            67

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            coagulation factor II [Mm.89048, NM_010168]

            Cell defence

            TTTCTTAAATC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            67

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            esterase 31-like [Mm.347422, NM_144511]

            Cell defence

            TTGTCCTCGTA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            61

            0a

            2a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            inter alpha-trypsin inhibitor, heavy chain 4 [Mm.211681, NM_018746]

            Cell defence

            GCGATGAAATC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            59

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            esterase 1 [Mm.88078, AI256598]

            Cell defence

            CTCATCGTATG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            57

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GGCACCTTCAC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            56

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            peptidoglycan recognition protein 4 [Mm.316644, XM_357978]

            Cell defence

            GAGCTGTTTCT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            56

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            cytochrome P450, family 2, subfamily c, polypeptide 40 [Mm.335940, NM_010004]

            Steroid hormone synthesis

            TTGCAAGGCTG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            46

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0

            albumin 1 [Mm.16773, AI747247]

            Cell defence

            GAGCTCTTCCT

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            45

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            cytochrome P450, family 2, subfamily d, polypeptide 26 [Mm.29064, NM_029562]

            Steroid hormone synthesis

            AGACCTTGGGA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            44

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            kininogen 2 [Mm.2160, NM_023125]

            Cell defence

            GTTGCTGACCG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            43

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            plasminogen [Mm.971, NM_008877]

            Protein synthesis

            AAAACAGAAAA

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            39

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            TGTGTTATTTT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            35

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            regucalcin [Mm.2118, NM_009060]

            Regulation of enzymatic activity

            AAAGTCCTCGA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            34

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            aldo-keto reductase family 1, member C6 [Mm.196666, NM_030611]

            Catalytic activity

            GATACAGACTA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            33

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GACACACACTA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            32

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            ACATTTCCAGA

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            28

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            2a

            0a

            0a

            0

            silica-induced gene 111 [Mm.330825, AV058272]

            promoting cell survival

            GGGACATTCGG

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            25

            0a

            1a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            solute carrier family 27 (fatty acid transporter), member 2 [Mm.290044, BC013442]

            Transport

            AAATTATTCCT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            24

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            major urinary protein 1 [Mm.335875, AW110035]

            Cell defence

               Adipose tissue

                                     

            CCAGCACTCAA

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            31

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            leptin [Mm.277072, NM_008493]

            Cell signaling

            TACCTTTCATA

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            29

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            7

            lectin, galactose binding, soluble 12 [Mm.298242, NM_019516]

            Cell division

               Lung

                                     

            CAAGGATCTAC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            85

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            surfactant associated protein D [Mm.1321, NM_009160]

            Cell defence

            TGTCTGCCTCT

            0a

            1a

            0a

            0a

            0a

            0a

            1a

            1a

            1a

            45

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            claudin 18 [Mm.35090, AK033657]

            Cell signaling

            ACCCACACTCC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            40

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            surfactant associated protein A1 [Mm.46062, NM_023134]

            Cell defence

            GCTCACAGAAA

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            35

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            palate, lung, and nasal epithelium carcinoma associated [Mm.268852, NM_011126]

            Cell defence

            GGCATCCCATT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            31

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            secretoglobin, family 3A, member 1 [Mm.22802, NM_170727]

            Cell defence

               Bone

                                     

            CTTTCCTGGGT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            144

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            proteoglycan 2, bone marrow [Mm.142727, NM_008920]

            Cell defence

            TTTTGGGCACA

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            1a

            0a

            0

            122

            0a

            0a

            0a

            0a

            0a

            4a

            0a

            0a

            0a

            0a

            0a

            0

            solute carrier family 4 (anion exchanger), member 1 [Mm.7248, NM_011403]

            transport

            TATGTGGACTG

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            2a

            1a

            0a

            59

            0a

            1a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0

            proteinase 3 [Mm.2364, NM_011178]

            Cell defence

            TGCCGCCGTCG

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            52

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            neutrophil elastase [Mm.262194, BX632826]

            Cell defence

            ACAGGAAGAGC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            39

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            eosinophil peroxidase [Mm.1315, NM_007946]

            Cell defence

            CCCTGGATCAA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            29

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            cathepsin G [Mm.4858, NM_007800]

            Cell defence

            CTGAGGTGGGC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            25

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            claudin 13 [Mm.86652, NM_020504]

            Cell signaling

            GAAATATTCAC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            25

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            membrane-spanning 4-domains, subfamily A, member 3 [Mm.119630, NM_133246]

            Cell defence

            AAAGTGTGACC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            25

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            72

            carbonic anhydrase 1 [Mm.273195, NM_009799]

            Cell defence

               Skeletal muscle

                                     

            TGGAACGAGCA

            0a

            1a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            1a

            68

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            TGGGCAGCCTT

            0a

            0a

            0a

            0a

            0a

            0a

            2a

            0a

            0a

            0a

            1a

            58

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            myosin light chain, phosphorylatable, fast skeletal muscle [Mm.14526, AV165375]

            Cell structure

            GACCTGAGGGC

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            1a

            0a

            0a

            0a

            41

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            ACCTCTATATA

            0a

            0a

            0a

            2a

            0a

            0a

            1a

            0a

            0a

            1a

            0a

            38

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            tropomyosin 3, gamma [Mm.240839, U04541]

            Cell structure

            a Significant difference vs. no. of tags shown in bold (p < 0,05)

            Table 5

            Specific genes expressed in the brain

                            

            Tissues from GEO and accession number

               

            Tag

            Testis

            Prostate

            Ovary

            Mammary gland

            Uterus

            Vagina

            Skin

            Liver

            Adipose tissue

            Lung

            Bone

            Skeletal muscle

            Cerebral cortex

            Hypothalamus

            Pituitary gland

            Mouse embryonic fibroblasts GSM7759

            Heart normal GSM106587

            Thymus normal GSM106596

            Bladder normal GSM106599

            Kidney normal GSM56242

            Spleen normal GSM106591

            Pancreas Normal GSM106592

            Intestine UniGene and EST expression (%)

            Description [UniGene cluster, GenBank Accession No]

            General function

               Cerebral cortex

                                     

            GTCGTCCTCTA

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            47

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0

            solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter), member 7 [Mm.255631, NM_182993]

            Transport

            TGACCTTGGCC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            41

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            gene model 748, (NCBI) [Mm.102203, AK122363]

            Protein binding and heme Binding

            GTACTTGGCTG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            24

            1a

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            synaptic vesicle glycoprotein 2 b [Mm.273082, NM_153579]

            Transporter activity

               Hypothalamus

                                     

            TTGGCAAGTCT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            198

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            RIKEN cDNA A230109K 23 gene [Mm.200361, BC048534]

            neurotransmitter or neuromodulator

            TGTGACGCTGG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            1a

            37

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            cocaine and amphetamine regulated transcript [Mm.75498, NM_013732]

            Cell signaling

            AGTTCCTTCGC

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            34

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            calbindin 2 [Mm.2755, NM_007586]

            Calciunion binding

            GGCCGCCGCGC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            33

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            hypocretin [Mm.10096, NM_010410]

            Cell signaling

               Pituitary gland

                                     

            AAGTGTCGCCG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            14963

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            growth horm one [Mm.343934, NM_008117]

            Cell signaling

            GGCGAGCTGAT

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            0a

            0a

            1496

            0a

            1a

            0a

            0a

            2a

            0a

            0a

            0

            Pro-opiomelanocortin-alpha [Mm.277996, NM_008895]

            Cell signaling

            GCGGGAAAAGC

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            1383

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            CTTGGGTGCAA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1307

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            prolactin [Mm.1270, NM_011164]

            Cell signaling

            AAGTGTCGCCT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            601

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            TTGGCGTCAAA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            436

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            AAGTGTCGCCA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            408

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            TCGGTTCTCTG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            329

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            ACGTACTTCCG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            222

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            CGCAGCGACGA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            218

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GCTGGGGCCCG

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            194

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            ACCCGCAGGTA

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            114

            0a

            0a

            0a

            0a

            0a

            0a

            0a

             

            NM

            Novel transcript

            GTCCGAGTACT

            2a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            1a

            0a

            0a

            0a

            0a

            75

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            luteinizing hormone beta [Mm.57061, NM_008497]

            Cell signaling

            TTACTCCTTAT

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            49

            0a

            0a

            0a

            0a

            0a

            0a

            0a

            0

            thyroid stimulating hormone, beta subunit [Mm.110730, NM_009432]

            Thyroid structure and metabolism

            a Significant difference vs. no. of tags shown in bold (p < 0,05)

            Discussion

            The most abundant housekeeping genes

            Quantitative gene expression data are often normalized to the expression levels of control or so-called housekeeping genes. An inherent assumption in the use of housekeeping genes is that expression of the genes remains constant in the tissues under investigation. Housekeeping genes do not vary in their expression levels during cell development, treatment, or disease state anomalies [16]. About 40 years ago, housekeeping genes were simply defined as those genes that are always expressed [1], also known as ubiquitous genes. However, for many experimental applications, we must make the difference between the housekeeping genes which are constantly expressed in all the tissues and the ubiquitous genes. According to the current study, the ubiquitous genes also previously called housekeeping genes such as PPIase, GAPDH, and beta-actin are expressed in all tissues with significant difference in their expression levels. On the other hand, the housekeeping genes eEF-2, ribosomal protein L37 and L38, proteasome (prosome, macropain) 26 subunit non-ATPase 4, eIF3, hypothetical protein, LRC member 8 also known as interleukin-8 receptor (IL-8R), and the RIKEN cDNA C030036P15, 1500016L11 and 2410104I19 genes are constantly expressed in all the tissues investigated. Our results are consistent with the previous report that ribosomal protein L37, proteasome and hypothetical protein are expressed at the same level in 11 human adult and fetal tissues [17]. In addition, except LRC member 8 and the RIKEN cDNAs, the transcripts reported as housekeeping genes in this study have also been previously presented as maintenance genes in a study investigating 11 human adult and fetal tissues [17]. Using the SAGE method, Velculescu et al also identified the same ubiquitous transcripts among nearly 1000 transcripts expressed at more than or equal to 5 copies par cell from 19 human tissues [18]. However, they did not apply the statistics to identify the constantly expressed genes. In the current study, we report eEF-2 as the housekeeping gene which is abundantly and constantly transcribed in all of the 15 tissues. Indeed, eEF-2 is known to be required for elongation in most eukaryotes [19]. Since eEF-2 does not vary in relative abundance in different tissues, this gene can be used as a standard or internal control. The constitutive expressions of ribosomal proteins L37 and L38 were observed in all the tissues. Our results are also consistent with the report that ribosomal protein L37 is constitutively expressed during transitions from quiescence to active cell proliferation or terminal differentiation in all tissues in rat and human [20]. Another study has shown that ribosomal protein L37 ranks amongst the fifteen most highly expressed housekeeping genes [21]. Furthermore, the present study identified LRC member 8 and eIF3 as housekeeping genes. LRC is known to play an important role in cell defence in all tissues. In mammals, the cell surface receptor encoded by LRC member 8 regulates the activity of lymphocytes and natural killer cells in order to provide protection against pathogens and parasites [22]. Previous studies have presented interleukin-12 receptor beta 2 [18] and interleukin-1 receptor-associated kinase [17] as ubiquitously expressed genes. No previous study had investigated LCR member 8 as a housekeeping gene or internal control. According to this study, we suggest for the first time interleukin-8 receptor as housekeeping gene or internal control since this transcript is ubiquitously expressed in all the tissues investigated. Proteasome (prosome, macropain) 26 subunit non-ATPase 4, the major proteolytic machinery responsible for degradation of both normal and damaged proteins has been identified as housekeeping gene. Our results are in agreement with the knowledge that proteasome is a multicatalytic complex found in all eukaryotic cells [23], and also with the report that proteasome ranks amongst the fifteen most constant housekeeping genes [21]. Therefore, our results are consistent with previous reports showing that housekeeping genes are generally involved in a variety of basic cellular functions, including intermediary metabolism, transcription, translation, cell signalling/communication and cell structure/motility [21]. In addition, the current study has identified three EST RIKEN cDNAs (C030036P15, 2410104I19 and 1500016L11) as housekeeping genes. We have also investigated three previously postulated housekeeping genes namely PPIase, beta-actin, and GAPDH [24] which are expressed with significant difference according to the current study. Our study is in agreement with the previous report that PPIase, beta-actin and GAPDH are maintenance genes expressed in 11 human adult and fetal tissues but are not expressed at the same level in these tissues [17]. GAPDH was especially highly expressed in the skeletal muscle. Beta-actin was also differentially expressed between the tissues. According to the present study, PPIase is more constantly expressed in all the tissues than beta-actin and GAPDH. This result can explain the previous report that PPIase is a better internal control than beta-actin and GAPDH [25].

            Specific genes expressed in the male sexual organs

            According to this study, the tissue-specific genes were observed in higher proportion in testis than any other tissues. The top 8 most abundant tissue-specific transcripts, namely protamine 2, transition protein 1, t-complex-associated testis expressed 3, the novel transcript GTGCCAGGAGA, tubulin alpha 3, diazepam binding inhibitor-like 5, lactate dehydrogenase 3 C chain sperm specific, and outer dense fiber of spermtails 2 are also the top 8 most abundant transcripts in this organ. These tissue-specific genes are all expressed in the specific stage of spermatogenesis. Other tissue-specific genes such as spermatogenic Zip 1 [26] and glyceraldehydes 3-phosphate dehydrogenase-spermatogenic [27], are expressed only during spermatogenesis. Translin associated factor X (Tsnax) interacting protein 1 is highly expressed in testis and in germ cells, suggesting a possible role in spermatogenesis [28]. Meanwhile, four-and-a-half-Lim-domain 5 is a LIM-only protein expressed exclusively in round spermatids [23], while kinesin family member 2b [29] and dipeptidase 3 [30] are expressed only in testis. The current study also reports the expression of testis specific genes such as ATPase class I type 8b member 3 which has hydrolase and phospholipid-translocating ATPase activity, and ATP-dependent aminophospholipid transporter which is exclusively expressed in the acrosomal region of spermatozoa [31]. In mammals, thioredoxins (trx) are generally ubiquitously expressed in all tissues, with the exception of sperm-specific trx (sptrx) which is exclusively detected in sperm cells [32]. The specific functions of these transcripts involved in spermatogenesis, explain the exclusive expression of these transcripts in the testis.

            We have identified some prostate specific genes such as microseminoprotein (beta-MSP), seminal vesicle protein secretion 2, seminal vesicle antigen (SVA) and mucin 10 (MUC10) which are involved in protein secretion, cell signalling and spermatogenesis. In addition, one novel transcript was observed to be solely expressed in the prostate. Beta-MSP, also known as prostate secretory protein of 94 amino acids (PSP94), is an abundant secretory protein of the prostate gland and is generally considered to be prostate tissue-specific [33]. Results from western and northern-blot analyses for various tissues had previously indicated that the seminal vesicle is the sole organ producing SVA which is able to induce autoantibody formation [34]. MUC10, the submandibular salivary gland (SMG) mucin which is the primary histodifferentiation product of submandibular epithelia, was observed as tissue-specific gene to the prostate in our study. MUC10 is a type 1 integral membrane protein with a disintegrin and metalloprotease domain (ADAM29) precursor involved in spermatogenesis and fertilization [35]. Other prostate tissue specific identified are CUB and zona pellucida-like domains 1 (Cuzd1), and serine peptidase inhibitor Kazal type 3. In mouse, the expression of a secretory protease inhibitor is constitutive in the pancreas but stimulated by testosterone in ventral prostate, coagulated gland and seminal vesicle [36]. Cuzd1 was identified as highly and predominantly expressed gene in mouse epididymis using a cDNA microarray [37]. Since prostate-specific antigen (PSA), also known as gamma-seminoprotein, is a serine protease produced and secreted abundantly by prostate cancer cells [38], we did not detect PSA in the current results on normal prostate. Probasin, previously postulated as tissue-specific gene in the prostate [39], was abundantly expressed in the prostate (1925 tags) and was also found in the liver (282 tags) according to the present study. These results may have important repercussion, since prostate tissue-specific genes expression is crucial for driving potentially therapeutic genes to target specifically to the prostate [39].

            Specific genes expressed in the female sexual organs

            Only two transcripts with unknown function and a novel transcript with sequence tag GTCAACACAGG were specifically detected in ovary. We report two transcripts, namely glycosylation cell adhesion molecule 1 (Glycam1) and the novel transcript with sequence tag TCCGGAGAAAA, which are expressed only in the mammary gland. Glycam1 has a protein binding activity and previous studies have reported that prolactin induced Glycam1 expression in primary mammary epithelial cell of mice [40].

            In uterus, three transcripts namely proline-rich acidic protein 1 (Prap1), hydroxysteroid 11-beta dehydrogenase 2 (Hsd11b2) and chloride channel calcium activated 3 (clca3) were characterized as tissue-specific. Northern analyses have demonstrated that Prap1 also known as pregnancy-specific uterine protein expression is limited to the pregnant uterus [41]. In the rat, the enzyme Hsd11b2 converts the glucocorticoid corticosterone into receptor-inactive 11 dehydrocorticosterone, thereby allowing preferential access of aldosterone to mineralocorticoid receptors. The effects of glucocorticoids are thus critically regulated by the intracellular enzyme Hsd11b2 which was shown here to be highly expressed in the uterus [42]. In addition, the information from UniGene and EST expression has shown that the transcripts identified in uterus are also expressed in intestine tissue.

            Two novel transcripts were observed to be tissue-specific to the vagina. Furthermore, the keratins such as keratin intermediate filament 16a, keratin complex 1 acidic gene 13 and keratin complex 2 basic gene 6 g, members of a family of fibrous structural proteins were also detected in high proportions in the vagina. Surprisingly, retinol binding protein 2, which functions in the intracellular transport of retinol, is detected only in vagina. According to the UniGene and EST databases, retinol binding protein 2 is also expressed in intestine tissue.

            Specific genes expressed in the skin, liver, adipose tissue, lung, bone and skeletal muscle

            The majority of transcripts specifically detected in the skin represent keratin. Moreover, the S100 calcium binding protein 17 and G protein-coupled receptor family C group 5 member D, both involved in cell signalling, were also specific to the skin. In addition, lymphocyte antigen 6 complex locus G6C, involved in cell defence, was also exclusively observed in the skin.

            The transcripts exclusive to the liver are involved in several functions such as cell defence, protein and steroid hormone synthesis, as well as transport and amino acid metabolism. We report in the current study that inter-alpha-trypsin inhibitor-4 (Itih-4) was exclusively detected in the liver. This result is in agreement with the report that Itih-4 is a liver-restricted member of the serine protease inhibitors family, with diverse functions such as anti-apoptotic action and matrix stabilization molecule that are important throughout development [43]. The present results also suggest that betaine-homocysteine methyltransferase (BHMT), cytochrome P450 family 2 subfamily d polypeptide 26 (Cyp2d26), microglobulin/bikunin precursor (AMBP) and plasminogen are solely expressed in the liver amongst the included organs. Previous studies have shown that BHMT [44] and Cyp2d26 [45] were expressed only liver and kidney, whereas strong expression of AMBP has been observed in developing hepatocyte, pancreas, kidney and gut [46]. The expression of plasminogen mRNA from hepatocyte is dependent on the cell density and stimulation [47] and is solely expressed in liver. Two mouse plasma proteins involved in cell defence, namely murinoglobulin 2 and kininogen 2 were exclusively expressed in the liver. Murinoglobulin is characterized as a single-chain proteinase inhibitor [48], while kininogen is known as a major acute phase protein whose levels increase 10–20 fold in response to an inflammatory challenge [49]. Traditionally, 4-hydroxyphenylpyruvic acid dioxygenase (HPD) has been considered as an enzyme primarily expressed in liver and to a lesser extent in kidney [50]. This previous study is agreement with the current study in which HPD is exclusively detected in the liver.

            Two transcripts, leptin and lectin galactose binding soluble 12 (Lgals12), were exclusively detected in adipose tissue. Leptin is a peptide hormone produced predominantly by white adipose tissue. Beside its key role in the regulation of food intake and energy expenditure, leptin is also involved in the pathogenesis of inflammatory and autoimmune disease [51]. On the other hand, Lgals12 also known as galectin-12 is preferentially expressed in mouse preadipocytes and is up-regulated when preadipocytes undergo cell cycle arrest [52].

            The transcripts specific to the lung are involved in cell defence, except claudin 18 which participates in cell signalling. The surfactant-associated proteins A (SP-A) and SP-D are members of a family of collagenous host defence lectins, designated collectins. The lung is the main site of SP-A and SP-D synthesis [53]. They are considered to be molecules of the innate immune system involved in the first line of defence of mucosal surfaces, especially in lung [53]. Another specific transcript is the palate lung and nasal epithelium clone (Plunc), also renamed Splunc1, which is a small secreted protein expressed in the oropharynx and upper airways of humans, mice, rats and cows. The members of the PLUNC family may be involved in the innate immune responses in regions of the mouth, nose and lung, which are sites of significant bacterial exposure [54]. Another transcript exclusively detected in the lung is secretoglobin family 3A member 1 which is thought to play a role in inflammation and/or epithelial cell differentiation in the lung. The mRNA encoding for this gene is expressed predominantly with low level in terminals bronchioles [55].

            The transcripts exclusively detected in the bone are involved in transport, cell structure, signalling and defence. The tissue-specific genes ascribed to proteoglycan 2 bone marrow and solute carrier family 4 (anion exchanger) member1 are highly and solely expressed in the bone. The other exclusive transcripts such as proteinase 3, neutrophil elastase, eosinophil peroxidase, cathepsin G and carbonic anhydrase 1 are involved in cell defence. Evidence from northern analysis has shown that proteinase 3 expression is primarily confined to the promyelocytic/myelocytic stage of bone marrow development [56]. The highly related serine protease known also as neutrophil elastase, proteinase 3 and cathepsin G are exclusively detected in promyelocytes and packaged in azurophil granules [57, 58], whereas carbonic anhydrase 1 is expressed in adult human and mouse erythroid cells and colon epithelia, from two distinct promoters [59]. Another transcript exclusively expressed in bone matches to haematopoietic cell-specific transmembrane-4 (HTm4), member of a family of membrane-spanning 4-domain proteins. It is known that HTm4 is expressed in hematopoietic tissue and is tightly regulated during the differentiation of hematopoietic stem cells [60].

            In the current study, the transcripts exclusively detected in skeletal muscle are novel transcripts except tropomyosin 3 gamma (Tpm3) and myosin light chain phosphorylatable fast skeletal muscle (MLC2) which are involved in cell structure. In the mice, the Tpm3 mRNA is found exclusively in the skeletal muscle but not in the cardiac tissue at any development stage, whereas, in human, Tpm3 is found in both adult heart and skeletal muscle [61, 62]. The specificity of MLC2, reported in the current study is in agreement with the previous study showing this gene expressed specifically in skeletal muscles of new-born and adult mice as well as rats [63].

            Specific genes expressed in the brain

            The current study reports that solute carrier family 17 (sodium-dependent inorganic phosphate cotransporter) member 7, also known as vesicular glutamate transporters (Vglut1), and synaptic vesicle glycoprotein 2 b (SV2B) as well as gene model 748 were exclusively expressed in cerebral cortex. This result is consistent with the report that Vglut1 mRNA is strongly expressed in the hippocampus and cerebellar cortex [64]. Vglut1 has been observed to play an unanticipated role in membrane trafficking at the nerve terminal [64]. SV2B is a protein highly related to a family of transporters. SV2B expression was observed to change during development; it is more widely expressed in the immature brain and is found in cells that have yet to establish synaptic contacts. SV2B is expressed in cerebral cortex, therefore further studies on the expression pattern of SV2B are needed to investigate the consistency with its function as a specific neurotransmitter transporter [65].

            We report that cocaine and amphetamine regulated transcript (CART), calbindin 2, hypocretin and RIKEN cDNA A230109K23 gene were exclusively detected in the hypothalamus. The protein calbindin 2 buffers intracellular calcium is speculated to be involved in the integration of neuronal signalling. CART encodes a hypothalamic neuropeptide precursor protein which has been identified and characterized in rat brain and later in human brain [66, 67]. Furthermore, hypocretin-1 and -2 (Hcrt-1 and Hcrt-2), also referred to as orexin-A and -B, are neuropeptides synthesized by a few thousand neurons in the lateral hypothalamus. Studies have hinted at a role of hypocretins in driving drug-seeking through activation of stress pathways in the brain [68]. Further investigation should be made in the characterization of RIKEN cDNA A230109K23.

            The transcripts exclusively expressed in the pituitary gland were also highly expressed in this gland. Except growth hormone, pro-opiomelanocortin-alpha, prolactin, luteinizing hormone beta (LH beta) and thyroid stimulating hormone beta subunit (TSH beta) also known as thyrotropin beta which are involved in cell signaling, the other specific genes to this gland had no match in public databases and therefore may represent novel transcripts. LH beta is essential for ovulation and reproductive fitness, and is well known to be synthesized specifically in pituitary gonadotropes [69]. In addition, this glycoprotein is essential for ovarian follicular development, maturation of the oocyte, steroidogenesis and ovulation. In males, LH beta is involved in regulation of steroidogenesis in the Leydig cells [70]. TSH is an anterior pituitary glycoprotein hormone which modulates thyroid hormone production by the thyroid gland. TSH is constituted of two subunits: the alpha subunit is held in common with the gonadotropins luteinizing hormone and follicle-stimulating hormone, and the beta subunit which is unique and confers biological specificity to the intact hormone [71].

            Conclusion

            Using SAGE strategy, this study has shown the housekeeping genes and the tissue-specific genes expressed in 15 intact tissues. The identified housekeeping genes can represent appropriate controls for RT-PCR and northern blot when comparing the expression levels of genes in several tissues. Several transcripts exclusively detected in a tissue are known to be tissue-specific genes according to previous studies. Furthermore, we have identified several new tissue-specific genes. These genes show well the specialty and particularity of each tissue. The tissue-specific genes can be used as a targeting agent in order to reach a particular tissue/organ. In addition, the current data can contribute significantly to comparative genomics in general and gene expression and regulation among different mouse tissues. Further studies will be needed to investigate other tissues to confirm the specific or housekeeping gene expressions. In addition, this study can serve as a basis for future studies on the novel transcripts and the transcripts with unclear functions despite their tissue specificity.

            Methods

            C57BL6 mice (12–15 week old) were obtained by Charles River Laboratories (St. Constant, Québec). They were housed in an air-condition room (19–25°C) with controlled lighting from 07:15 to 19:15 h and were given free access to food (Lab Rodent Diet No. 5002) and water. The GDX and ADX groups had surgery 7 days before death. The intact, GDX and ADX groups received vehicle solution (0.4% (w/v) Methocel A15LV Premium/5% ethanol) 24 hours before sacrifice. DHT (0.1 mg) was injected 3 h prior to killing in GDX+DHT groups. ADX mice received sodium chloride (0.9 g/dl) in their drinking water after the surgery. Gcc (corticosterone, 0.1 mg per mouse) was subcutaneously injected into ADX mice, and the tissues were harvested 3 h after the injection. All animal experimentation was conducted in accord with the requirements of the Canadian Council on Animal Care. All the tissues were from male mice except for female sexual tissues. The tissues were dissected from 15–51 mice, frozen in liquid nitrogen and stocked at -80°C until analysis.

            Total RNA was isolated from tissues by using the RNA extraction kit (TRIzol Reagent, Invitrogen Canada Inc., Burlington, ON). Approximately 5 μg of mRNA was extracted with Oligotex mRNA Mini Kit (Qiagen Inc., Mississauga, ON). The SAGE method was performed as previously described [13, 14]. In brief, double-strand cDNA was synthesized from the mRNA using a biotinylated (T)18 primer and cDNA synthesis kit (Invitrogen Canada Inc.). The cDNA libraries were digested with the restriction enzyme NlaIII (New England Biolabs Inc., Pickering, ON). The 3'-terminal cDNA fragments were captured using streptavidin-coated magnetic beads (Dynal, Biotech LLC, Brown Deer, WI). After ligation of 2 annealed linker pairs, the cDNA fragments were digested with BsmFI (New England Biolabs Inc.). The blunting kit from Takara Bio Inc. (Otsu, Japan) was used for the blunting and ligation of the two tag populations. The resulting ligation products were amplified by PCR and digested with NlaIII. The band containing the ditags was extracted from the 12% polyacrylamid gel. Using T4 ligase (Invitrogen Canada Inc.), the ditags were self-ligated to form concatemers that were cloned into SphI site of pUC19. White colonies were screened by PCR and agarose gel to select long inserts for automated sequencing (Applied Biosystems 3730, Foster City, CA). The data discussed in this publication have been deposited in NCBIs Gene Expression Omnibus [72] and are accessible through GEO Series accession number GSE5915. The sequence and occurrence of each of the transcript tags has been determined using the software SAGEana.pl, an updated version of SAGEparser.pl [73]. To identify the transcripts, we have generated a SAGEmap of 11 bp tags by the script SAGEmap.pl using the NCBI 10 bp tags SAGEmap, as well as the UniGene Clusters and mitochondrial mRNA sequences. The tag sequences must perfectly match at the last NlaIII restriction site (CATG) at the 3' end of a given transcript. To overcome the lower quality of some EST sequences, the tags that did not identify a well-characterized mRNA were required to match at least two ESTs in the same UniGene Cluster including one EST with a known polyA tail. To identify the transcripts, the sequences of 15 bp SAGE tags were matched with public databases. The tag numbers normalized by 100000 are shown in Tables 1, 2, 3, 4, 5.

            The SAGE method has very good reproducibility [73]. However, several factors can affect this reproducibility such as the failure to provide relevant matching statistics. When a tag matches multiple genes, it is impossible to know the number of copies which are contributed by each gene since the matching stastitic is giving by the mixture of all contributing genes. However, using a 15 bp (CATG + 11 bp) tag, the SAGEparser program decreases the number of multiple matches and increases the number of tags which uniquely identify a transcript [73]. Therefore, the tags matching multiple genes were excluded from the current report. We used the comparative count display (CCD) test to identify the transcripts that were significantly (p ≤ 0.05) differentially expressed between the groups with more than 2-fold change. CCD test performs a key-by-key comparison of two key-count distributions by generating a probability that the frequency of any key in the distribution differs by more than a given fold factor from the other distribution. This statistical test has already been described elsewhere [74]. We have used the web site source at Stantford [75] to add the comparison of the tissue-specific genes with the UniGene and EST expression database information.

            Declarations

            Acknowledgements

            This work was supported by Genome Québec and Genome Canada. Mayumi Yoshioka is supported by the Heart and Stroke Foundation of Canada (HSFC), the Canadian Institute of Health Research (CIHR) and the Canadian Diabetes Association (CDA) as a post-doctoral fellow. Dr Jonny St-Amand is an investigator supported by the Fonds de la recherche en santé du Québec (FRSQ).

            Authors’ Affiliations

            (1)
            Functional Genomics Laboratory, Molecular Endocrinology and Oncology Research Center, Department of Anatomy and Physiology, Laval University Medical Center (CHUL),Laval University

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            Copyright

            © Kouadjo et al. 2007

            This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://​creativecommons.​org/​licenses/​by/​2.​0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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