Table 3

Differentially expressed transcripts located to QTL-regions for bone 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

* 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

1 Chromosome and positions (in Megabases) of transcripts are based on build 2.1 of the chicken genome

2 Where applicable, Ensembl gene from which transcripts are derived

3 Gene annotation. If applicable, gene name or name of putative orthologue are presented. NA = Not applicable, due to lacking annotation.

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.

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.

6 M-values log2(fold change) for M, F and P-comparison, respectively. Negative M-values indicate lower expression in WL.

Rubin et al. BMC Genomics 2007 8:208   doi:10.1186/1471-2164-8-208