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Table 1 Genes altered significantly in liver by starvation

From: Starvation alters the liver transcriptome of the innate immune response in Atlantic salmon (Salmo salar)

TRAITS IDENTIFIER1

ACC2

AFL3

ASL4

PSL5

 

Identity6

  

FC A

FC B

FC C

group7

 

Blood and serum proteins

liv_stb_J4D11_sti_tra_sub_0p_11S

AM397499

  

3.17

Cu

(P80961) Antifreeze protein LS-12 precursor

liv_ali_02H02_abe_tra_sub_0p_11C

AM402609

  

2.92

Cu

Type-4 ice-structuring protein precursor (Antifreeze protein type IV)

tes_opk_14E17_osl_sgp_std_5p_11S

CK899203

  

2.26

Cu

(P29788) Vitronectin precursor (Serum spreading factor) (S-protein)

int_oss_T5O22_osl_sal_std_5p_11C

CK885870

 

-2.15

-2.74

BCd

(P14527) Hemoglobin alpha-4 subunit (Hemoglobin alpha-4 chain) (Alpha-4-globin)

spl_sts_19B11_sti_sal_std_5p_12S

AJ425729

  

-3.71

Cd

(P02019) Hemoglobin alpha-1 subunit (Hemoglobin alpha-1 chain) (Alpha-1-globin)

mus_snm_10F04_osl_tra_nrc_5p_11C

EG648831

  

-4.16

Cd

(P02142) Hemoglobin beta-1 subunit

swi_rpk_74B22_osl_sgp_std_5p_11C

CK896319

  

-6.95

Cd

(Q01584) Lipocalin precursor

Energy metabolism

swi_rpk_74M05_osl_sgp_std_5p_11S

CK895001

  

3.68

Cu

isocitrate dehydrogenase 2 (NADP+) mitochondrial

gil_oss_52N23_osl_sal_std_5p_11C

CK879377

  

3.05

Cu

(Q9N2D5) Glyceraldehyde-3-phosphate dehydrogenase (EC 1.2.1.12) (GAPDH)

liv_ali_06G02_abe_tra_sub_0p_11S

AM402930

  

2.05

Cu

Bos taurus mono(ADP-ribosyl)transferase (ART1) mRNA

int_oss_T5A05_osl_sal_std_5p_11C

CK885697

  

-2.17

Cd

(P48163) NADP-dependent malic enzyme (EC 1.1.1.40) (NADP-ME) (Malic enzyme1)

pit_cpi_C1C04_car_tra_sub_0p_11C

No Acc

  

-2.39

Cd

glyoxalase 1

tes_tsr_02H11_gal_sal_std_5p_11C

BM413811

  

-3.06

Cd

(Q8BH95) Enoyl-CoA hydratase mitochondrial precursor (EC 4.2.1.17)

Stress response

kid_aki_05A08_abe_tra_sub_0p_11C

AM042306

29.57

12.79

3.63

ABCu

(P06761) 78 kDa glucose-regulated protein precursor (GRP 78) (BiP)

hrt_opk_04E05_osl_sgp_std_5p_11C

CK883188

15.54

7.86

2.57

ABCu

DnaJ-like subfamily B member 11

gil_oss_GHB16_osl_sal_std_5p_11C

CN181053

  

2.30

Cu

(P08110) Endoplasmin precursor (Heat shock 108 kDa protein) (Transferrin-binding protein)

int_oss_T5B18_osl_sal_std_5p_11C

CK885962

2.31

 

2.27

ACu

(P30710) Epididymal secretory glutathione peroxidase precursor (EC 1.11.1.9)

liv_opk_12F09_osl_sgp_std_5p_11C

CK888938

  

2.12

Cu

glutathione peroxidase 3

int_oss_T4K02_osl_sal_std_5p_11C

CK884637

  

2.10

Cu

(O57521) Heat shock protein HSP 90-beta

gil_rpk_76A21_osl_sgp_std_5p_11C

CK878328

  

2.06

Cu

(P08294) Extracellular superoxide dismutase [Cu-Zn] precursor (EC 1.15.1.1)

hrt_opk_08M01_osl_sgp_std_5p_11C

CK899423

-2.39

 

-2.47

ACd

thioredoxin interacting protein

bra_snb_06F02_osl_tra_nrc_5p_11C

EG647964

  

-2.84

Cd

(Q4AEH7) Glutathione peroxidase 2 (EC 1.11.1.9)

Immune related

swi_rpk_74F07_osl_sgp_std_5p_11C

CK896920

  

9.77

Cu

(Q9ES30) Complement C1q tumor necrosis factor-related protein 3 precursor

liv_ali_02G01_abe_tra_sub_0p_11C

AM402595

  

5.33

Cu

C-type MBL-2 protein

liv_lrr_01C04_gal_sal_std_5p_11C

No Acc

  

2.91

Cu

(Q02988) Lectin precursor

eye_opk_20I02_osl_sgp_std_5p_11S

CO471610

7.56

2.97

2.86

ABCu

(P27797) Calreticulin precursor (CRP55) (Calregulin)

liv_dis_D1E12_abe_tra_sub_0p_11N

AM049479

16.18

6.74

2.79

ABCu

similar to catechol-O-methyltransferase domain containing 1

liv_dis_D4H02_abe_tra_sub_0p_11N

AM049741

14.11

7.30

2.59

ABCu

precerebellin-like protein

liv_dis_D4B06_abe_tra_sub_0p_11N

AM049686

  

2.04

Cu

(Q9WUW3) Complement factor I precursor (EC 3.4.21.45) (C3B/C4B inactivator)

liv_dis_D1G04_abe_tra_sub_0p_11N

AM049505

2.65

 

2.00

ACu

(O88803) Leukocyte cell-derived chemotaxin 2 precursor

kid_aki_05H02_abe_tra_sub_0p_11C

AM042371

  

-2.03

Cd

(Q801Y3) Hepcidin 1 precursor

tes_tsa_01C01_gal_sal_std_5p_11C

No Acc

  

-2.58

Cd

liver-expressed antimicrobial peptide 2 isoform A precursor

liv_lrr_01C06_gal_sal_std_5p_11C

No Acc.

-2.05

 

-2.59

ACd

(P04186) Complement factor B precursor (EC 3.4.21.47)

liv_dis_D4A07_abe_tra_sub_0p_11N

AM049678

  

-3.09

Cd

C type lectin receptor A

eye_rpk_73M16_osl_sgp_std_5p_11C

CK875442

  

-3.82

Cd

TTRAP_BRARETRAF and TNF receptor-associated protein homolog

gil_oss_G6N16_osl_sal_std_5p_11C

CK877483

-2.31

 

-4.15

ACd

nuclear factor kappa-B 1

liv_opk_12I14_osl_sgp_std_5p_11S

CK889507

  

-4.65

Cd

(P80429) Serotransferrin II precursor (Siderophilin II) (STF II)

kid_aki_04G07_abe_tra_sub_0p_11C

AM042284

  

-10.17

Cd

(P81491) Serum amyloid A-5 protein

Lipid and steroid metabolism

bra_opk_07F18_osl_sgp_std_5p_11S

CK875291

5.39

 

4.62

ACu

(O35760) Isopentenyl-diphosphate delta-isomerase 1 (EC 5.3.3.2)

swi_rpk_74J22_osl_sgp_std_5p_11C

CK896123

  

3.91

Cu

similar to Elongation of very long chain fatty acids protein 2

liv_opk_12J23_osl_sgp_std_5p_11C

CK888142

4.94

 

3.35

ACu

AF232215Salvelinus fontinalis steroidogenic acute regulatory protein (StAR)

hrt_opk_06O21_osl_sgp_std_5p_11C

CK874989

  

3.13

Cu

(O88822) Lathosterol oxidase (EC 1.3.3.2) (Lathosterol 5-desaturase)

bra_snb_09B09_osl_tra_nrc_5p_11S

EG647637

  

2.77

Cu

squalene monooxygenase

liv_ali_01E09_abe_tra_sub_0p_11S

AM402497

  

2.74

Cu

(P23228) Hydroxymethylglutaryl-CoA synthase cytoplasmic (EC 2.3.3.10)

bra_bfo_02D04_fou_sal_nrc_5p_11S

DW588272

  

2.36

Cu

(P37268) Squalene synthetase (EC 2.5.1.21)

kid_opk_01A09_osl_sgp_std_5p_11S

CK887294

  

-2.18

Cd

(O54939) Estradiol 17-beta-dehydrogenase 3 (EC 1.1.1.62)

bra_bfo_13G03_fou_sal_nrp_5p_11M

DW589986

  

-4.35

Cd

(Q92038) Acyl-CoA desaturase (EC 1.14.19.1) (Delta(9)-desaturase)

ova_opk_10D15_osl_sgp_std_5p_11C

CK891273

-5.23

 

-4.51

ACd

(Q18268) Phosphodiesterase delta-like protein

Amino acid metabolism

swi_rpk_74K12_osl_sgp_std_5p_11C

CK895973

  

2.74

Cu

betaine-homocysteine methyltransferase

bra_bfo_15H06_fou_sal_nrp_5p_11M

DW590158

  

2.73

Cu

(P46410) Glutamine synthetase (EC 6.3.1.2) (Glutamate--ammonia ligase) (GS)

liv_ali_03E06_abe_tra_sub_0p_11C

AM402665

  

2.63

Cu

alanine-glyoxylate aminotransferase

mus_snm_07H11_osl_tra_nrc_5p_11C

EG648581

  

2.63

Cu

(P82264) GLutamate dehydrogenase (EC 1.4.1.3) (GDH)

liv_ali_02E10_abe_tra_sub_0p_11C

AM402574

  

2.13

Cu

(Q866Y3) N-acetylmuramoyl-L-alanine amidase precursor (EC 3.5.1.28)

liv_opk_12F15_osl_sgp_std_5p_11C

CK888977

  

2.00

Cu

(P16930) Fumarylacetoacetase (EC 3.7.1.2) (Fumarylacetoacetate hydrolase)

Protein degradation

ova_oyr_02D04_gal_sal_std_5p_11S

BM414061

4.13

2.09

4.07

ABCu

(P97571) Calpain-1 catalytic subunit (EC 3.4.22.52)

mus_mfo_14E10_fou_sal_nrp_5p_11M

DW592075

  

-2.12

Cd

(Q9JHW0) Proteasome subunit beta type 7 precursor (EC 3.4.25.1)

liv_ali_04H04_abe_tra_sub_0p_11C

AM402779

  

-2.22

Cd

(P62193) 26S protease regulatory subunit 4 (Proteasome 26S subunit ATPase 1)

hkd_opk_03C15_osl_sgp_std_5p_11S

CK881845

  

-2.31

Cd

(P18242) Cathepsin D precursor (EC 3.4.23.5)

spl_sts_03D12_sti_sal_std_5p_11C

AJ425020

  

-2.43

Cd

(Q9H944) Ubiquitin-specific protease homolog 49 (TRF-proximal protein homolog)

tes_opk_13P17_osl_sgp_std_5p_11S

CK898961

-2.99

 

-3.60

ACd

(Q92743) Serine protease HTRA1 precursor (EC 3.4.21.-)

int_oss_T6A14_osl_sal_std_5p_11C

CK884021

  

-3.66

Cd

(P62972) Ubiquitin

int_rpk_78A08_osl_sgp_std_5p_11S

CK885620

-7.97

 

-8.17

ACd

(Q04592) Proprotein convertase subtilisin/kexin type 5 precursor (EC 3.4.21.-)

Protein synthesis

gil_rpk_75O01_osl_sgp_std_5p_11C

CK878136

  

-2.29

Cd

(P47198) 60S ribosomal protein L22

gil_cgi_E3H04_car_tra_sub_0p_11N

No Acc

-2.39

 

-2.40

ACd

(Q9DCH4) Eukaryotic translation initiation factor 3 subunit 5

bra_bfo_04H04_fou_sal_nrc_3p_11C

DW588554

  

-2.45

Cd

AF390021_1glutamine synthetase

mus_mfo_13G09_fou_sal_nrp_5p_11S

DW591963

  

-2.67

Cd

(P25007) Peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8)

tes_tsr_03A07_gal_sal_std_5p_11C

BM413900

  

-3.28

Cd

(Q7ZYS1) 60S ribosomal protein L19

spl_sts_17H08_sti_sal_std_5p_11C

AJ425625

-3.58

 

-4.97

ACd

(P63326) 40S ribosomal protein S10

int_oss_T6A03_osl_sal_std_5p_11C

CK884084

-9.32

 

-8.66

ACd

rRNA promoter binding protein

Cell structure

int_oss_T4C19_osl_sal_std_5p_11C

CK885060

  

-2.15

Cd

collagen a3(I)

int_oss_THA07_osl_sal_std_5p_11C

CN181319

  

-2.13

Cd

Oncorhynchus mykiss COL1A3 mRNA for collagen a3(I) complete cds

int_rpk_78C22_osl_sgp_std_5p_11C

CK885437

  

-2.76

Cd

(O00423) Echinoderm microtubule-associated protein-like 1 (EMAP-1)

mus_snm_03C07_sti_tra_nrc_5p_11C

EG649361

  

-2.76

Cd

(O93484) Collagen alpha 2(I) chain precursor

ova_oyr_04F11_gal_sal_std_5p_11S

BM414013

  

-3.96

Cd

(P14105) Myosin-9 (Myosin heavy chain nonmuscle IIa)

  1. List of selected mRNAs found up and down regulated resulting from starvation and grouped according to functional classes (shown in bold). The selection was based on manual assignment of function and genes with greatest fold difference in expression are presented, the genes that are down regulated are denoted by (-) value. In this table the genes within each group are ordered by expression level following starvation (PSL). If the genes were significantly altered in the infection these values are also given. The genes shown were significant at P < 0.001 following correction for multiple tests and greater than 2 fold change. 1Indicates the unique code for the feature on the microarray, 2Accession number of the cDNA sequence, if "No Acc" the TRAITS web page. 3Fold change for genes increased in expression following Aeromonas salmonicida infection in fish fed a normal diet (AFLvsPFL). 4Fold change for genes increased in expression following A. salmonicida infection in fish starved prior to infection (ASLvsPSL). 5Fold change for genes increased expression following 28 days starvation. 6Identity of the cDNA as determined by BlastX and BlastN searches. 7This indicates if this gene is up regulated in one or more other experiments, Ad (AFL), Bd (ASL), Cd (PSL), ABd (AFL+ASL), ABCd (AFL+ASL+PSL). The complete list of genes can be found in Additional file Table S1.