PMC

Heat map representation of (a) TF and (b) TcoF expression in 14 bovine tissues. Rows represent tissues’ expression profile. Each column represents a TF in (a) and a TcoF in (b), where the color corresponds to the expression level (yellow for low expression, red for high expression, and white for not expressed).

Heat map representation of TF-TcoF coexpression in 14 bovine tissues (white blood cells, kidney, jejunum, liver, ampulla, pons, spleen, semitendinosus muscle, gallbladder, caruncular regions ipsilateral - car ips - to the corpeus luteum, mesenteric lymph nodes, caruncular regions contralateral - car con - to the corpeus luteum, heart, cerebral cortex). Columns represent tissues grouped by their expression profile. Each row represents a TF-TcoF pair.

Heat map representation of the conservation of bovine TFs across 21 eukaryotic species. Rows represent the TFs and columns represent the species; both are hierarchically clustered according to the presence (green) or absence (white) of orthologues in the respective species. The color bar on the right indicates whether the TFs are predominantly present in mammals (pink), vertebrates (orange), Metazoans (yellow) or all analyzed eukaryotes (green).

Identification of bovine TFs: 1. Update of the human TF reference repertoire; 2. Compilation of reliable DNA-binding domains (DBDs) as in Vaquerizas et al., augmented by DBDs found in alternative human and mouse TF databases (AnimalTFDB, DBD, Cis-BP); 3. Identification of putative bovine TFs using the list of reliable DBDs; 4. Manual curation of the putative bovine TFs by examining orthology to human TFs, protein function, experimental evidence and similarity of domain arrangement. Resulting high-confidence bovine TFs are divided in the evidence classes “a” and “b”.

Classification of TFs according to their DNA-binding domain. The families found were: Homeodomain, Basic-leucine zipper (bZIP), Helix-loop-helix (HLH), p53, Nuclear hormone receptor (NHR), Forhead, High mobility group (HMG), Erythroblast Transformation Specific (ETS), MAD, POU-specific domain (POU), Helix-turn-heliz (HTH), IPT, SAND, Transcription factor E2F/dimerisation partner (TDP), Interferon Regulation Factor (IRF), Paired domain (PAX), Zinc finger GATA type (ZNF-GATA), Zinc finger BED type (ZNF-BED), CP2 transcription factor (CP2), DM, Signal Transducers and Activators of Transcription (STAT), Transcription Factor AP-2 (AP2), MADs-box, DNA-binding Regulatory Factor (RFX), other. The domains classified as other were: Heat shock factor (HSF)-type, Zinc finger CCCH-type, TEA/ATTS, Zinc finger NF-X1-type, Octamer-binding transcription factor, SANT/Myb domain, Hypoxia-inducible factor-1 alpha, Cold-shock protein, DNA-binding, Transcription factor Otx1, Transcription regulator GCM domain, Transcription factor CBF/NF-Y/archaeal histone domain, CG-1 DNA-binding domain, CCAAT-binding factor, Putative DNA-binding domain, Myelin transcription factor 1, Beta-trefoil DNA-binding domain.