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Table 1 The 40 most extreme genes by Phenotypic Impact Factor in High FE versus Low FE birds. These 40 genes have been reordered manually into functional groupings. The absolute DE expressed as a fold change has also been reported

From: Progesterone signalling in broiler skeletal muscle is associated with divergent feed efficiency

Gene symbol Gene name Fold Change HFE/LFE Gene function
MB Myoglobin 4.10 Down Iron storage, highly expressed in red, slow fibres
MYH15 Myosin heavy chain 15, slow 4.46 Down Slow twitch fibre isoform
TPM3 Tropomyosin 3, slow 2.67 Down Slow twitch fibre isoform
MYOZ2 Myozenin 2, slow 2.54 Down Slow twitch fibre isoform
TNNI1 Troponin I type I, slow 3.36 Down Slow twitch fibre isoform
PLN Phospholamban 2.78 Down Highly expressed in slow twitch fibres, substrate for cAMP-dependent protein kinase.
COL3A1 Collagen 3A1 2.09 Down ECM
COL12A1 Collagen 12A1 2.66 Down ECM
FN1 Fibronectin 1 2.01 Down ECM
BMP5 Bone morphogenetic protein 5 4.23 Down Negative regulation of IGF1 signaling
RSFR Leukocyte ribonuclease A2 2.56 Down Angiogenesis
LY86 Lymphocyte antigen 86 2.42 Down Inflammation, apoptosis
MGAT5B beta-1,6-N-acetylglucosaminyltransferase 3.51 Down Synthesis of cell surface n-glycans, ECM
NES Nestin 2.64 Down Expressed in nerve cells, implies motor unit
APOA1 Apolipoprotein A1 2.27 Down Promotes cholesterol efflux from tissues. Highly expressed in liver.
MGP Matrix Gla protein 1.84 Down ECM
IGJ Immunoglobulin J polypeptide 2.21 Down Little known
SEPP1 Selenoprotein P 2.19 Down Extracellular glycoprotein and antioxidant
CA3 Carbonic anhydrase III 1.93 Down Response to oxidative stress, expressed at high levels in skeletal muscle
CTSS Cathepsin S 2.24 Down Lysosomal cysteine proteinase
H2AFY Histone family member Y 2.47 Up Associated with lipogenic genes
HIG2A (ENSGALG00000003348) Hypoxia-inducible domain family 2.15 Up Little known
TESK1 Testis specific kinase 1.95 Up Cell matrix communication
C11ORF89 * Uannotated ORF 2.44 Up Unannotated
CKMT1 Creatine kinase mitochondrial 1 1.63 Up Creatine metabolism, muscle energy supply
CNTFR Ciliary Neurotrophic factor 2.20 Up Skeletal muscle development
ENKD1 Enkurin domain containing 2.19 Up Cytoplasmic microtubule protein
CA4 Carbonic anhydrase 4 3.95 Up Respiration, acid base balance, expressed on luminal surface of capillaries
INSIG1 Insulin induced gene 1 1.92 Up Regulation of intracellular cholesterol concentration and steroid biosynthesis
TTPA Tocopherol (alpha) binding protein 2.84 Up Binds alpha-tocopherol a form of vitamin E, response to pH
LINGO1 Leucine rich repeat and Ig domain containing 1 1.72 Up Nervous system development
DCUN1D5 Defective in cullin neddylation 1, domain containing 5 2.10 Up Ubiquitin conjugating enzyme binding
SNCG1 Synuclein gamma 3.40 Up Synapse protein
C16ORF45 Unannotated ORF 1.88 Up Protein function unknown
LIPG Endothelial lipase 2.20 Up Lipoprotein metabolism and vascular biology
(ENSGALG00000028983) BLASTS to HOXA9 2.33 Up Transcription Factor
(ENSGALG00000027955) BLASTS to MHC 2.31 Up MHC immune function
BFSP1 Beaded filament structural protein 1 3.16 Up Cytoskeletal structure
MYL2_1 (MYL2A) MYL2A 3.39 Up Thought to be more highly expressed in cardiac muscle i.e. slow fibres
MYBPH Myosin binding protein H 1.53 Up Fast isoform
  1. * We further explored the possible function of the gene encoding an unannotated Open Reading Frame (ORF) C11ORF89, given it was in the top 20 upregulated genes in the HFE birds. The entry in GeneCards (under the alias PRR33) predicts the ORF to translate into a large protein containing regions of low complexity and comparative analysis suggests that the protein was present in the ancestor of the chordates. It is located in the G. gallus genome adjacent to TNNT3 and TNNI2, and cellular compartment analysis (http://compartments.jensenlab.org/) suggests there is moderate evidence it is a cytoskeletal protein