TY - JOUR T1 - Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes JF - bioRxiv DO - 10.1101/085654 SP - 085654 AU - Naoki Osato Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/04/21/085654.abstract N2 - Background Transcriptional target genes show functional enrichment of genes. However, how many and how significantly transcriptional target genes include functional enrichments are still unclear. To address these issues, I predicted human transcriptional target genes using open chromatin regions, ChIP-seq data and DNA binding sequences of transcription factors in databases, and examined functional enrichment and gene expression level of putative transcriptional target genes.Results Gene Ontology annotations showed four times larger numbers of functional enrichments in putative transcriptional target genes than gene expression information alone. To compare the number of functional enrichments of putative transcriptional target genes between cells or search conditions, I normalized the number of functional enrichment by calculating its ratios in the total number of transcriptional target genes. With this analysis, native putative transcriptional target genes showed the largest normalized number of functional enrichments, compared with target genes including 5 – 60% of randomly selected genes. The normalized number of functional enrichments was changed according to the criteria of enhancer-promoter interactions such as distance from transcriptional start sites and orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites showed significantly higher normalized number of functional enrichments than the other orientations. The median expression level of transcriptional target genes changed according to the criteria of enhancer-promoter assignments (i.e. interactions) and was correlated with the changes of the normalized number of functional enrichments of transcriptional target genes.Conclusions Human putative transcriptional target genes showed significant functional enrichments. The normalized number of functional enrichments of human putative transcriptional target genes changed according to the criteria of enhancer-promoter assignments and correlated with the median expression level of the target genes. These analyses and characters of human putative transcriptional target genes would be useful to examine the criteria of enhancer-promoter assignments and to predict the novel mechanisms and factors such as DNA binding proteins and DNA sequences of enhancer-promoter interactions.TFtranscription factorsTFBStranscription factor binding sitesTSStranscriptional start sitesENCODEencyclopedia of DNA elementsChIP-seqChIP-sequencing, chromatin immunoprecipitation followed by massively parallel DNA sequencingRNA-seqRNA-sequencingEPApromoter and extended regions for enhancer-promoter associationFRforward-reverseRFreverse-forwardFFforward-forwardRRreverse-reverse ER -