摘要
A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach--using sequence conservation across cattle, human and dog and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection （MGC） annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCKI, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the lllumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http：//bfgl. anri.barc.usda.gov/BovineTFBS/or http：//199.133.54.77/BovineTFBS.
A resource that provides candidate transcription factor binding sites （TFBSs） does not currently exist for cattle. Such data is necessary, as predicted sites may serve as excellent starting locations for future omics studies to develop transcriptional regulation hypotheses. In order to generate this resource, we employed a phylogenetic footprinting approach--using sequence conservation across cattle, human and dog and position-specific scoring matrices to identify 379,333 putative TFBSs upstream of nearly 8000 Mammalian Gene Collection （MGC） annotated genes within the cattle genome. Comparisons of our predictions to known binding site loci within the PCKI, ACTA1 and G6PC promoter regions revealed 75% sensitivity for our method of discovery. Additionally, we intersected our predictions with known cattle SNP variants in dbSNP and on the lllumina BovineHD 770k and Bos 1 SNP chips, finding 7534, 444 and 346 overlaps, respectively. Due to our stringent filtering criteria, these results represent high quality predictions of putative TFBSs within the cattle genome. All binding site predictions are freely available at http：//bfgl. anri.barc.usda.gov/BovineTFBS/or http：//199.133.54.77/BovineTFBS.
基金
supported by the National Research Institute and the Agricultural and Food Research Initiative(Grant No. 2007-35205-17869 and 2011-67015-30183) from the United States Department of Agriculture Cooperative State Research, Education and Extension Service(now the National Institute of Food and Agriculture)
Project form the US Department of Agriculture--Agricultural Research Service(ARS)(Grant No. 1265-31000-098-00)
