Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

Naoki Osato
2018 BMC Genomics  
11 Background: Transcriptional target genes show functional enrichment of genes. 12 However, how many and how significantly transcriptional target genes include 13 functional enrichments are still unclear. To address these issues, I predicted human 14 transcriptional target genes using open chromatin regions, ChIP-seq data and DNA 15 binding sequences of transcription factors in databases, and examined functional 16 enrichment and gene expression level of putative transcriptional target genes.
more » ... 7 18 Results: Gene Ontology annotations showed four times larger numbers of functional 19 enrichments in putative transcriptional target genes than gene expression information 20 alone, independent of transcriptional target genes. To compare the number of functional 21 enrichments of putative transcriptional target genes between cells or search conditions, I 22 normalized the number of functional enrichment by calculating its ratios in the total 23 number of transcriptional target genes. With this analysis, native putative transcriptional 24 target genes showed the largest normalized number of functional enrichments, 25 compared with target genes including 5 -60% of randomly selected genes. The 26 normalized number of functional enrichments was changed according to the criteria of 27 enhancer-promoter interactions such as distance from transcriptional start sites and 28 orientation of CTCF-binding sites. Forward-reverse orientation of CTCF-binding sites 29 showed significantly higher normalized number of functional enrichments than the 30 other orientations. Journal papers showed that the top five frequent functional 31 enrichments were related to the cellular functions in the three cell types. The median 32 . CC-BY 4.0 International license not peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was . http://dx.doi.org/10.1101/085654 doi: bioRxiv preprint first posted online Nov. 4, 2016; expression level of transcriptional target genes changed according to the criteria of 33 enhancer-promoter assignments (i.e. interactions) and was correlated with the changes 34 of the normalized number of functional enrichments of transcriptional target genes. 35 36 Conclusions: Human putative transcriptional target genes showed significant functional 37 enrichments. Functional enrichments were related to the cellular functions. The 38 normalized number of functional enrichments of human putative transcriptional target 39 genes changed according to the criteria of enhancer-promoter assignments and 40 correlated with the median expression level of the target genes. These analyses and 41 characters of human putative transcriptional target genes would be useful to examine 42 the criteria of enhancer-promoter assignments and to predict the novel mechanisms and 43 factors such as DNA binding proteins and DNA sequences of enhancer-promoter 44 interactions. 45 46
doi:10.1186/s12864-017-4339-5 pmid:29363429 pmcid:PMC5780744 fatcat:pbtqjkr6gzeb7jwhefwfwbhdka