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Table 2 Top table of 85 microarray probes identified as differentially expressed (q < 0.015) in all three contrasts between White Leghorn and red junglefowl (male vs. male, female vs. female and all WL vs. all RJ)

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

GenBank ID Ensembl gene ID Position Annotation 1 M 2 q-value 3
[GenBank:CN217913] ENSGALG00000018770 Un: 28.3 Mb NA -0.40 3.2E-12
[GenBank:CN229911] ENSGALG00000013482 Un: 21.4 Mb NA -0.38 9.8E-11
[GenBank:CN228750] ENSGALG00000016807 1: 140.6 Mb Lim and senescent cell-antigen like domains 1 (LIMS1) -0.86 9.8E-11
[GenBank:CN225543] ENSGALG00000012809 2: 67.1 Mb Peroxisomal D3,D2-enoyl-CoA isomerase (PECI) -0.43 2.7 E-09
[GenBank:CN223571] ENSGALG00000014429 Un: 60.2 Mb similar to trans-golgi network protein 2 (TGOLN2) -0.56 5.0 E-09
[GenBank:CN219393] ENSGALG00000008774 3: 104.9 Mb Paralogue to PBX/knotted 1 homeobox 1 (PKNOX1) -0.35 5.5 E-09
[GenBank:BU410845] ENSGALG00000005079 6: 16.5 Mb Vinculin (VCL) -0.46 8.9 E-09
[GenBank:CN232734] ENSGALG00000016171 2: 151.3 Mb protein-tyrosine kinase 2 (PTK2) -0.34 1.7 E-08
[GenBank:CN218021] ENSGALG00000018770 Un: 28.3 Mb NA -0.41 2.1 E-08
[GenBank:CN225644] ENSGALG00000002659 17: 7.9 Mb WD repeat domain 5 protein (WDR5) -0.45 1.4 E-07
[GenBank:CN238026] ENSGALG00000000978 21: 889 kb Similar to KIAA0562 0.44 2.2 E-07
[GenBank:CN234176] ENSGALG00000016171 2: 151.4 Mb protein-tyrosine kinase 2 (PTK2) -0.39 2.4 E-07
[GenBank:CN236144] ENSGALG00000003797 7: 4.5 Mb NA 0.70 2.6 E-07
[GenBank:CN236164] ENSGALG00000015289 3: 69.8 Mb Armadillo repeat domain containing 2 (ARMC2) 0.56 2.6 E-07
[GenBank:CN229608] ENSGALG00000007968 1: 641 kb Putative orthologue to FAM40B -0.25 2.6 E-07
[GenBank:CN236322] ENSGALG00000003078 18: 6.0 Mb similar to monocyte to macrophage differentiation-associated (MMD) -0.51 2.6 E-07
[GenBank:CN225020] ENSGALG00000020260 4: 16.7 Mb progesterone receptor membrane component 1 (PGRMC1) -0.44 2.7 E-07
[GenBank:CN235998] ENSGALG00000006921 15: 9.3 Mb developmentally regulated GTP binding protein 1 (DRG1) 0.32 3.8 E-07
[GenBank:CN224535] ENSGALG00000016323 1: 121.5 Mb Putative orthologue to Pyruvate dehydrogenase kinase isozyme 3 (PDK3) 0.26 6.1 E-07
[GenBank:CN233472] ENSGALG00000005079 6: 16.5 Mb Vinculin (VCL) -0.34 6.1 E-07
[GenBank:CN222595] ENSGALG00000004818 15: 6.5 Mb 60S ribosomal protein L6 (RPL6) -0.45 6.1 E-07
[GenBank:CN238036] ENSGALG00000000978 21: 889 kb Similar to KIAA0562 0.40 7.9 E-07
[GenBank:CN226213]   1: 130.1 Mb NA -0.40 2.9 E-06
[GenBank:CN229954] ENSGALG00000007941 5: 21.2 Mb Similar to human C11orf74 protein 0.17 3.4 E-06
[GenBank:CN217480] ENSGALG00000003107 11: 2.1 Mb Autocrine motility factor receptor, isoform 2 (AMFR) -0.15 3.4 E-06
[GenBank:CN221901]   NA NA -0.63 4.0 E-06
[GenBank:CN225340] ENSGALG00000022549 Un: 49.4 Mb Putative orthologue to V-set and transmembrane domain containing (VSTM1) -0.67 4.3 E-06
[GenBank:CN227456]   2: 3.8 Mb NA -0.59 4.3 E-06
[GenBank:CN218246] ENSGALG00000024009 5: 680 kb NA 0.24 5.5 E-06
[GenBank:CN232981] ENSGALG00000000212 Z: 43.0 Mb Growth arrest and DNA-damage-inducible protein GADD45 beta (GADD45B) -0.28 5.5 E-06
[GenBank:CN237898]   26: 4.8 Mb NA -0.25 5.5 E-06
[GenBank:CN230682]   Un: 33.1 Mb NA 0.37 6.0 E-06
[GenBank:CN230471] ENSGALG00000015972 1: 108.8 Mb interferon gamma receptor 2 (IFNGR2) -0.36 6.0 E-06
[GenBank:CN223293]   NA NA 0.34 6.2 E-06
[GenBank:BU303036] ENSGALG00000013094 2: 83.0 Mb Dopa decarboxylase (DDC) -0.34 1.3 E-05
[GenBank:CN218709] ENSGALG00000001564 19: 3.3 Mb Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (SERCA3) -0.33 1.3 E-05
[GenBank:CN226292]   4: 51.2 Mb NA -0.46 1.6 E-05
[GenBank:CN226240] ENSGALG00000022145 Un: 45.0 Mb Cell division cycle associated 8 (CDCA8) -0.67 1.6 E-05
[GenBank:CN237835] ENSGALG00000001573 19: 3.3 Mb Putative orthologue to purinergic receptor P2X ligand-gated ion channel 1 (P2RX1) -0.30 2.0 E-05
[GenBank:CN218191] ENSGALG00000015960 4: 89.4 Mb Putative orthologue to Ribose-5-phosphate isomerase (RPIA) -0.22 2.5 E-05
[GenBank:CN218073] ENSGALG00000008285 1: 13.9 Mb NA -0.33 2.5 E-05
[GenBank:CN225607]   3: 134.8 Mb NA 0.29 2.7 E-05
[GenBank:CN224144] ENSGALG00000001024 21: 960 kb Putative orthologue to Protein FAM79A 0.22 3.1 E-05
[GenBank:CN234653] ENSGALG00000004414 5: 1.15 Mb Putative orthologue to leucine zipper protein 2 (LUZP2) -0.79 3.1 E-05
[GenBank:CN232675] ENSGALG00000002384 7: 289 kb NA 0.19 3.6 E-05
[GenBank:CN229033]   1: 6.3 Mb NA -0.35 3.6 E-05
[GenBank:CN220674] ENSGALG00000015842 1: 107.9 Mb Putative orthologue to T-cell lymphoma invasion and metastasis 1 (TIAM1) -0.22 3.6 E-05
[GenBank:CN225767] ENSGALG00000008686 2: 19.8 Mb Putative orthologue to tRNA (cytosine-5-)-methyltransferase (TRDMT1) 0.26 3.8 E-05
[GenBank:CN228075] ENSGALG00000014880 Z: 14.2 Mb Putative orthologue to Poly ADP-ribose polymerase 8 (PARP8) -0.40 3.9 E-05
[GenBank:CN236904] ENSGALG00000004823 8: 8.4 Mb Ring finger protein 2 (RNF2) 0.19 4.4 E-05
[GenBank:CN227721] ENSGALG00000024253 Un: 21.8 Mb NA 0.29 4.6 E-05
[GenBank:CN219383]   Un: 57.4 Mb NA -0.21 4.8 E-05
[GenBank:CN218286]   1: 16.9 Mb NA 0.35 5.9 E-05
[GenBank:BU383276]   7: 5.02 Mb NA -0.45 6.2 E-05
[GenBank:CN228342] ENSGALG00000004981 12: 5.12 Mb tRNA-splicing endonuclease subunit Sen2 (TSEN2) -0.20 6.5 E-05
[GenBank:CN219649]   18: 9.2 Mb NA -0.39 6.5 E-05
[GenBank:CN235129] ENSGALG00000015976 1: 108.8 Mb Putative orthologue to Transmembrane protein 50B (TMEM50B) -0.36 6.9 E-05
[GenBank:CN222892] ENSGALG00000011834 4: 55.1 Mb Nucleoside diphosphate-linked moiety X motif 6 (NUDT6) 0.27 6.9 E-05
[GenBank:CN227190] ENSGALG00000015637 2: 122.5 Mb Putative orthologue to 60S ribosomal protein L7 (RPL7) -0.43 8.8 E-05
[GenBank:CN235632] ENSGALG00000014011 1: 69.3 Mb Putative orthologue to lymphoid-restricted membrane protein (LRMP) -0.35 9.3 E-05
[GenBank:CN232385] ENSGALG00000009822 3: 23.0 Mb NA 0.18 9.9 E-05
[GenBank:CN217382] ENSGALG00000005587 5: 9.7 Mb Eukaryotic translation initiation factor 4 gamma 2 (EIF4G2) -0.29 1.2 E-04
[GenBank:CN222062]   11: 8.3 Mb NA 0.26 1.4 E-04
[GenBank:CN218760] ENSGALG00000011031 8: 29.0 Mb Janus kinase 1 (JAK1) -0.32 1.8 E-04
[GenBank:CN230192]   * gi| 212798| ± 0.97 2.1 E-04
[GenBank:CN227388]   * gi| 28971912| ± 1.24 2.5 E-04
[GenBank:CN234584]   * gi| 118084693| ± 1.22 2.5 E-04
[GenBank:CN222174] ENSGALG00000007378 1: 79.9 Mb NA 0.20 2.9 E-04
[GenBank:CN219692]   23: 1.4 Mb NA 0.24 3.0 E-04
[GenBank:CN217559] ENSGALG00000009621 Un: 20.4 Mb Putative orthologue to gamma actin (ACTG) -0.53 3.5 E-04
[GenBank:CN222240] ENSGALG00000014494 Un: 42.5 Mb Putative orthologue to vacuolar protein sorting 16 (VPS16) 0.17 3.8 E-04
[GenBank:CN235771] ENSGALG00000008285 1: 13.9 Mb Putative orthologue to N-acyl-phosphatidylethanolamine-hydrolyzingphospholipase D (NP_945341.2) -0.28 3.8 E-04
[GenBank:CN227888] ENSGALG00000006545 Un: 33.2 Mb Ran-binding protein 2 (RanBP2) -0.42 3.8 E-04
[GenBank:DQ211077] ENSGALG00000024372 * 16: 40 kb * MHC class I antigen (Fragment) -0.70 4.4 E-04
[GenBank:CN228106] ENSGALG00000022764   NA 0.13 4.6 E-04
[GenBank:CN217063] ENSGALG00000009201 14: 15.0 Mb Putative orthologue to Cyclin F (CCNF) -0.29 5.7 E-04
[GenBank:CN234096] ENSGALG00000014339 Un: 11.3 Mb Putative orthologue to Biogenesis of lysosome-related organelles complex-1 subunit 3 (BLOC1S3) -0.42 6.0 E-04
[GenBank:CN220094] ENSGALG00000016241 1: 115.9 Mb Putative orthologue to ATPase, H+ transporting, lysosomal, accessory protein 2 (ATP6AP2) 0.37 9.4 E-04
[GenBank:CN219753]   20: 5.5 Mb NA 0.25 9.9 E-04
[GenBank:CN231414] ENSGALG00000016813 1: 141.1 Mb NA 0.51 0.0011
[GenBank:CN233509]   1: 172.6 Mb NA -0.22 0.0019
[GenBank:CN218972] ENSGALG00000007178 5: 18.0 Mb Putative orthologue of fatty acid desaturase 2 (FADS2) -0.32 0.0034
[GenBank:CN231098] ENSGALG00000015122 2: 107.4 Mb Putative orthologue of TAF4b RNA polymerase II, TATAbox binding protein (TBP)-associated factor, 105 kDa (TAF4B) 0.56 0.0046
[GenBank:CN222925] ENSGALG00000011164 2: 33.7 Mb NA -0.46 0.012
[GenBank:CN218459] ENSGALG00000016340 1: 121.7 Mb Putative orthologue of Eukaryotic translation initiationfactor 2 subunit 3 (EIF2S3) -0.20 0.014
  1. 1 Annotation: Gene name if available. Putative orthologues to ensemble chicken transcripts are presented when no gene name is available. NA = No annotation and is presented in cases where neither is applicable.
  2. 2 M-value: Log2(Fold difference in expression) in contrast all WL versus all RJ. Positive M-values indicate more expression in White Leghorn.
  3. 3 q-value: FDR-adjusted p-value from sex independent contrast between WL and RJ. * BLAST search of probe sequence against the chicken genome produced multiple hits± Represents endogenous retroviral elements. Highest scoring BLAST hit is presented.