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Table 3 Differentially expressed transcripts located to QTL-regions for bone traits

From: Differential gene expression in femoral bone from red junglefowl and domestic chicken, differing for bone phenotypic traits

Genbank ID Pos.1 Ensembl gene2 Annotation 3 QTL4 DE 5 M-values6
[GenBank:CN234847] 1:30.2 ENSGALG00000009494 Putative orthologue to human THAP domain containing 5 (THAP5) ecirc1 M 0.36
-0.02
0.18
[GenBank:CN232736] 1:31.3 ENSGALG00000009547 Putative orthologue to human periphilin 1 (PPHLN1) ecirc1 F P -0.09
-0.29
-0.19
[GenBank:CN220162] 1:32.4   NA ecirc1 P -0.17
-0.19
-0.18
[GenBank:CN223165] 1:34.4 ± ENSGALG00000009762 Gag polyprotein ecirc1 M P 0.49
0.32
0.40
[GenBank:CN217879] 1:35.5 ENSGALG00000009829 Putative orthologue to Ribosomal protein L18 A (RPL18A) ecirc1 P -0.20
-0.34
-0.27
[GenBank:BU128191] 1:35.7 ENSGALG00000009867 Wnt inhibitory factor 1 (WIF1) * ecirc1 F 0.17
0.68
0.43
[GenBank:BU118286] 1:35.7 ENSGALG00000009867 Wnt inhibitory factor 1 (WIF1) * ecirc1 F 0.15
0.64
0.39
[GenBank:CN224091] 1:43.5 ENSGALG00000010992 Putative orthologue to Solute carrier family 6, member 15 (SLC6A15) nc-bmd1 P 0.26
0.14
0.20
[GenBank:CN221299] 1:47.0   NA nc-bmd1 M P 0.41
0.21
0.31
[GenBank:CN226131] 1:47.2 ENSGALG00000011325 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 12 (NDUFA12) nc-bmd1 M 0.30
-0.00
0.14
[GenBank:CN223612] 1:49.5 ENSGALG00000011651 Putative orthologue to ADP-ribosylation factor-like 1 (ARL1) nc-bmd1 P 0.36
0.35
0.36
[GenBank:CN229035] 1:49.9 ENSGALG00000023235 NA nc-bmd1 M P -0.33
-0.27
-0.30
[GenBank:CN217578] 1:50.1 ENSGALG00000011798 Putative orthologue to heme-binding protein1 (HEBP1) nc-bmd1 M 0.71
0.42
0.55
[GenBank:CN230393] 1:51.0 ENSGALG00000011856 NA nc-bmd1 P 0.16
0.14
0.15
[GenBank:CN224774] 1:51.0 ENSGALG00000011859 Eye-globin [UniProt:Q5QRU6] nc-bmd1 P -0.20
-0.20
-0.20
[GenBank:CN219273] 1:51.8 ENSGALG00000012013 Putative orthologue to Solute carrier family 25, member 17 (SLC25A17) nc-bmd1 F 0.08
0.31
0.20
[GenBank:CN223291] 1:52.6   NA nc-bmd1 M P 0.48
0.26
0.37
[GenBank:CN221539] 1:52.6   NA nc-bmd1 P 0.21
0.30
0.26
[GenBank:CN223252] 1:52.7 ENSGALG00000019317 Putative orthologue to Josephin domain-containing 1 (JOSD1) nc-bmd1 M P 0.29
0.17
0.23
[GenBank:CN230599] 1:52.8   NA nc-bmd1 M -0.16
0.00
-0.08
[GenBank:CN235584] 1:52.8 ENSGALG00000012247 Putative homologue to DEAD/H BOX 17 (DDX17) nc-bmd1 F 0.09
-0.30
-0.10
[GenBank:CN231378] 1:52.8   NA nc-bmd1 P 0.15
0.13
0.14
[GenBank:CN220256] 1:52.9 ENSGALG00000012272 NA nc-bmd1 P 0.38
0.36
0.37
[GenBank:CN221882] 1:53.3 ENSGALG00000012456 Putative orthologue to Ras-related C3 botulinum toxin substrate 2 (RAC2) nc-bmd1 M -0.52
-0.15
-0.34
[GenBank:CN234446] 1:55.1   NA nc-bmd1 F P -0.20
-0.32
-0.26
[GenBank:CN227045] 1:55.3 ENSGALG00000012569 Putative orthologue to F-box only protein 7 (FBXO7) nc-bmd1 F -0.00
-0.13
-0.07
[GenBank:CN226884] 1:55.3 ENSGALG00000012619 NA nc-bmd1 F -0.02
-0.12
-0.07
[GenBank:CN223798] 1:56.2   NA nc-bmd1 M P 0.42
0.27
0.35
[GenBank:CN219664] 1:59.3   NA nc-bmd1 M P 0.41
0.23
0.32
[GenBank:CN222216] 1:61.2   NA nc-bmd1 M 0.18
-0.05
0.06
[GenBank:CN231349] 1:63.0   NA nc-bmd1 P 0.11
0.13
0.12
[GenBank:CN222823] 1:63.7   NA nc-bmd1 P 0.31
0.22
0.26
[GenBank:BU329405] 1:63.9 ENSGALG00000013039 BH3-interacting domain death agonist (BID) nc-bmd1 M P -0.14
-0.11
-0.12
[GenBank:CN219432] 2:57.4   NA bmd1 M P -0.25
-0.19
-0.22
[GenBank:CN233407] 2:63.3   NA bmd1 M 0.24
0.02
0.13
[GenBank:CN231046] 2:65.5 ENSGALG00000012784 Putative orthologue to Thioredoxin domain-containing protein 5 (TXNDC5) bmd1 M 0.29
0.09
0.19
[GenBank:BU318588] 2:66.2 ENSGALG00000012802 Putative orthologue to human Coagulation factor XIII A chain precursor (F13A1) bmd1 P -0.44
-0.46
-0.46
[GenBank:CN225543] 2:67.0 ENSGALG00000012809 Peroxisomal D3,D2-enoyl-CoA isomerase (PECI) bmd1 ALL -0.42
-0.42
-0.42
[GenBank:CN222249] 2:78.1 ENSGALG00000012965 Putative orthologue to family with sequence similarity 105, member A (FAM105A) bmd1 P -0.14
-0.17
-0.15
[GenBank:CN227494] 2:80.5 ENSGALG00000013041 Putative orthologue to T-complex protein 1 subunit epsilon (CCT5) bmd1 M -0.27
-0.06
-0.16
[GenBank:BU303036] 2:83.0 ENSGALG00000013094 Dopa decarboxylase (DDC) bmd1 ALL -0.26
-0.40
-0.33
[GenBank:CN232630] 2:85.8   NA bmd1 M -0.21
-0.01
-0.11
[GenBank:CN217215] 20:1.4 ENSGALG00000001903 Putative orthologue to microtubule-associated protein 1, light chain 3 alpha (MAP1LC3A) tors M 0.34
0.07
0.20
[GenBank:CN222258] 20:1.7   NA tors P 0.18
0.22
0.20
[GenBank:CN220691] 20:3.8   NA tors F P -0.15
-0.19
-0.17
[GenBank:CN221589] 20:5.2 ENSGALG00000004143 Putative orthologue to tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta isoform (YWHAB) tors M P -0.23
-0.06
-0.15
[GenBank:CN227581] 20:5.3 ENSGALG00000023846 NA tors F 0.01
0.16
0.09
[GenBank:CN236828] 20:5.3 ENSGALG00000004170 Adenosine deaminase (ADA) tors F P -0.27
-0.69
-0.48
[GenBank:CN235806] 20:5.3   NA tors M -0.26
-0.09
-0.18
[GenBank:CN219753] 20:5.5   NA tors ALL 0.21
0.28
0.25
[GenBank:CN232642] 20:8.4 ENSGALG00000005635 Transcription factor-like 5 (TCFL5) tors P -0.12
-0.11
-0.11
[GenBank:CN227039] 20:8.4 ENSGALG00000005652 NA tors P -0.12
-0.22
-0.17
[GenBank:CN220570] 20:9.0 ENSGALG00000005849 Putative orthologue to chromosome 20 open reading frame 149 (C20orf149) tors M -0.38
0.01
-0.18
[GenBank:CN218403] 20:9.0 ENSGALG00000005887   tors M P 0.52
0.26
0.39
[GenBank:CN223304] 20:9.5 ENSGALG00000006046 Putative orthologue to DnaJ homolog subfamily Cmember 5 (DNAJC5) tors M P 0.37
0.29
0.33
[GenBank:CN231170] 20:9.8   NA tors P 0.15
0.23
0.19
[GenBank:BU199756] 20:10.2 ENSGALG00000006657 Microtubule-associated protein RP/EB family member 1 (MAPRE1) * tors M P -0.20
-0.13
-0.16
[GenBank:CN228069] 20:10.2 ENSGALG00000006657 Microtubule-associated protein RP/EB family member 1 (MAPRE1) * tors M P -0.35
-0.18
-0.26
[GenBank:CN236120] 20:10.4 ENSGALG00000006817 Putative orthologue to catenin, beta like 1 (CTNNBL1) tors P 0.08
0.10
0.09
[GenBank:CN232968] 20:11.9 ENSGALG00000007768 Putative orthologue to Aurora kinase A (AURKA) tors P 0.34
0.43
0.39
  1. * WIF1 and MAPRE1 are represented by two clones on the microarray± [GenBank:CN223165] may represent a retroviral element and may be present also elsewhere in the genome
  2. 1 Chromosome and positions (in Megabases) of transcripts are based on build 2.1 of the chicken genome
  3. 2 Where applicable, Ensembl gene from which transcripts are derived
  4. 3 Gene annotation. If applicable, gene name or name of putative orthologue are presented. NA = Not applicable, due to lacking annotation.
  5. 4 Previously identified QTLs for traits of femoral bone. ecirc1 = sex independent QTL for endosteal circumference, nc-bmd1 = female specific QTL for noncortical bone mineral density (BMD), bmd1 = female specific QTL for various measurements of BMD, tors1 = female specific QTL affecting femoral elasticity in torsion test.
  6. 5 The comparison between WL and RJ in which transcript was found differentially expressed (FDR-adjusted p-value < 0.0015. M = males, F = females, P = population (all WL compared to all RJ), ALL = M, F and P.
  7. 6 M-values log2(fold change) for M, F and P-comparison, respectively. Negative M-values indicate lower expression in WL.