Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes
Abstract 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 re...
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| Format: | Article |
| Language: | English |
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BMC
2018-01-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-017-4339-5 |
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| author | Naoki Osato |
| author_facet | Naoki Osato |
| author_sort | Naoki Osato |
| collection | DOAJ |
| description | Abstract 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, independent of transcriptional target genes. 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. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. 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. Functional enrichments were related to the cellular functions. 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. |
| first_indexed | 2024-04-13T21:45:31Z |
| format | Article |
| id | doaj.art-8f1665cbab0045d791dbb81dcfbbe61b |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-13T21:45:31Z |
| publishDate | 2018-01-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-8f1665cbab0045d791dbb81dcfbbe61b2022-12-22T02:28:35ZengBMCBMC Genomics1471-21642018-01-0119S113515110.1186/s12864-017-4339-5Characteristics of functional enrichment and gene expression level of human putative transcriptional target genesNaoki Osato0Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka UniversityAbstract 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, independent of transcriptional target genes. 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. Journal papers showed that the top five frequent functional enrichments were related to the cellular functions in the three cell types. 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. Functional enrichments were related to the cellular functions. 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.http://link.springer.com/article/10.1186/s12864-017-4339-5Transcriptional target genesFunctional enrichmentGene expressionTranscription factorsEnhancerOpen chromatin regions |
| spellingShingle | Naoki Osato Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes BMC Genomics Transcriptional target genes Functional enrichment Gene expression Transcription factors Enhancer Open chromatin regions |
| title | Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| title_full | Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| title_fullStr | Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| title_full_unstemmed | Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| title_short | Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| title_sort | characteristics of functional enrichment and gene expression level of human putative transcriptional target genes |
| topic | Transcriptional target genes Functional enrichment Gene expression Transcription factors Enhancer Open chromatin regions |
| url | http://link.springer.com/article/10.1186/s12864-017-4339-5 |
| work_keys_str_mv | AT naokiosato characteristicsoffunctionalenrichmentandgeneexpressionlevelofhumanputativetranscriptionaltargetgenes |