Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data.
Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental tech...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2020-01-01
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| Series: | PLoS ONE |
| Online Access: | https://doi.org/10.1371/journal.pone.0243332 |
| _version_ | 1818681358365491200 |
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| author | Ruslan N Sharipov Yury V Kondrakhin Anna S Ryabova Ivan S Yevshin Fedor A Kolpakov |
| author_facet | Ruslan N Sharipov Yury V Kondrakhin Anna S Ryabova Ivan S Yevshin Fedor A Kolpakov |
| author_sort | Ruslan N Sharipov |
| collection | DOAJ |
| description | Creating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental technology studying genome-wide interactions between TFs and DNA. We assessed the transcriptional significance of cell line-specific features using regression analysis of ChIP-Seq datasets from the GTRD database and transcriptional start site (TSS) activities from the FANTOM5 expression atlas. For this purpose, we initially generated a large number of features that were defined as the presence or absence of TFs in different promoter regions around TSSs. Using feature selection and regression analysis, we identified sets of the most important TFs that affect expression activity of TSSs in human cell lines such as HepG2, K562 and HEK293. We demonstrated that some TFs can be classified as repressors and activators depending on their location relative to TSS. |
| first_indexed | 2024-12-17T10:01:41Z |
| format | Article |
| id | doaj.art-c10f56ae1f2942dfa6e287bfa9e455fa |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-17T10:01:41Z |
| publishDate | 2020-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-c10f56ae1f2942dfa6e287bfa9e455fa2022-12-21T21:53:16ZengPublic Library of Science (PLoS)PLoS ONE1932-62032020-01-011512e024333210.1371/journal.pone.0243332Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data.Ruslan N SharipovYury V KondrakhinAnna S RyabovaIvan S YevshinFedor A KolpakovCreating a complete picture of the regulation of transcription seems to be an urgent task of modern biology. Regulation of transcription is a complex process carried out by transcription factors (TFs) and auxiliary proteins. Over the past decade, ChIP-Seq has become the most common experimental technology studying genome-wide interactions between TFs and DNA. We assessed the transcriptional significance of cell line-specific features using regression analysis of ChIP-Seq datasets from the GTRD database and transcriptional start site (TSS) activities from the FANTOM5 expression atlas. For this purpose, we initially generated a large number of features that were defined as the presence or absence of TFs in different promoter regions around TSSs. Using feature selection and regression analysis, we identified sets of the most important TFs that affect expression activity of TSSs in human cell lines such as HepG2, K562 and HEK293. We demonstrated that some TFs can be classified as repressors and activators depending on their location relative to TSS.https://doi.org/10.1371/journal.pone.0243332 |
| spellingShingle | Ruslan N Sharipov Yury V Kondrakhin Anna S Ryabova Ivan S Yevshin Fedor A Kolpakov Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. PLoS ONE |
| title | Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. |
| title_full | Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. |
| title_fullStr | Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. |
| title_full_unstemmed | Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. |
| title_short | Assessment of transcriptional importance of cell line-specific features based on GTRD and FANTOM5 data. |
| title_sort | assessment of transcriptional importance of cell line specific features based on gtrd and fantom5 data |
| url | https://doi.org/10.1371/journal.pone.0243332 |
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