ArticleGenomics, proteomics & bioinformatics2013
Identification of candidate transcription factor binding sites in the cattle genome.
Article in Genomics, proteomics & bioinformatics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- In silico identification of variations in microRNAs with a potential impact on dairy traits using whole ruminant genome SNP datasets.Scientific reports · 2021Article
- Polymorphisms in theCanine medicine and genetics · 2020Article
- Computational identification of tissue-specific transcription factor cooperation in ten cattle tissues.PloS one · 2019Article
- Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits.BMC genomics · 2018Article
- Widespread modulation of gene expression by copy number variation in skeletal muscle.Scientific reports · 2018Article
- Prioritizing single-nucleotide polymorphisms and variants associated with clinical mastitis.Advances and applications in bioinformatics and chemistry : AABC · 2017Article
- Signatures of Selection for Environmental Adaptation and Zebu × Taurine Hybrid Fitness in East African Shorthorn Zebu.Frontiers in genetics · 2017Article
- Regulatory and coding genome regions are enriched for trait associated variants in dairy and beef cattle.BMC genomics · 2014Article
- Gene regulatory networks in the genomics era.Genomics, proteomics & bioinformatics · 2013Article
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
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 PCK1, 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 Illumina 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.
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