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Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform
A core transcriptional regulatory circuit (CRC) is a group of interconnected auto-regulating transcription factors (TFs) that form loops and can be identified by super-enhancers (SEs). Studies have indicated that CRCs play an important role in defining cellular identity and determining cellular fate...
Autores principales: | , , , , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Frontiers Media S.A.
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546348/ https://www.ncbi.nlm.nih.gov/pubmed/34712617 http://dx.doi.org/10.3389/fonc.2021.761700 |
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author | Wei, Ling Chen, Jiaxin Song, Chao Zhang, Yuexin Zhang, Yimeng Xu, Mingcong Feng, Chenchen Gao, Yu Qian, Fengcui Wang, Qiuyu Shang, Desi Zhou, Xinyuan Zhu, Jiang Wang, Xiaopeng Jia, Yijie Liu, Jiaqi Zhu, Yanbing Li, Chunquan |
author_facet | Wei, Ling Chen, Jiaxin Song, Chao Zhang, Yuexin Zhang, Yimeng Xu, Mingcong Feng, Chenchen Gao, Yu Qian, Fengcui Wang, Qiuyu Shang, Desi Zhou, Xinyuan Zhu, Jiang Wang, Xiaopeng Jia, Yijie Liu, Jiaqi Zhu, Yanbing Li, Chunquan |
author_sort | Wei, Ling |
collection | PubMed |
description | A core transcriptional regulatory circuit (CRC) is a group of interconnected auto-regulating transcription factors (TFs) that form loops and can be identified by super-enhancers (SEs). Studies have indicated that CRCs play an important role in defining cellular identity and determining cellular fate. Additionally, core TFs in CRCs are regulators of cell-type-specific transcriptional regulation. However, a global view of CRC properties across various cancer types has not been generated. Thus, we integrated paired cancer ATAC-seq and H3K27ac ChIP-seq data for specific cell lines to develop the Cancer CRC (http://bio.liclab.net/Cancer_crc/index.html). This platform documented 94,108 cancer CRCs, including 325 core TFs. The cancer CRC also provided the “SE active core TFs analysis” and “TF enrichment analysis” tools to identify potentially key TFs in cancer. In addition, we performed a comprehensive analysis of core TFs in various cancer types to reveal conserved and cancer-specific TFs. |
format | Online Article Text |
id | pubmed-8546348 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-85463482021-10-27 Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform Wei, Ling Chen, Jiaxin Song, Chao Zhang, Yuexin Zhang, Yimeng Xu, Mingcong Feng, Chenchen Gao, Yu Qian, Fengcui Wang, Qiuyu Shang, Desi Zhou, Xinyuan Zhu, Jiang Wang, Xiaopeng Jia, Yijie Liu, Jiaqi Zhu, Yanbing Li, Chunquan Front Oncol Oncology A core transcriptional regulatory circuit (CRC) is a group of interconnected auto-regulating transcription factors (TFs) that form loops and can be identified by super-enhancers (SEs). Studies have indicated that CRCs play an important role in defining cellular identity and determining cellular fate. Additionally, core TFs in CRCs are regulators of cell-type-specific transcriptional regulation. However, a global view of CRC properties across various cancer types has not been generated. Thus, we integrated paired cancer ATAC-seq and H3K27ac ChIP-seq data for specific cell lines to develop the Cancer CRC (http://bio.liclab.net/Cancer_crc/index.html). This platform documented 94,108 cancer CRCs, including 325 core TFs. The cancer CRC also provided the “SE active core TFs analysis” and “TF enrichment analysis” tools to identify potentially key TFs in cancer. In addition, we performed a comprehensive analysis of core TFs in various cancer types to reveal conserved and cancer-specific TFs. Frontiers Media S.A. 2021-10-12 /pmc/articles/PMC8546348/ /pubmed/34712617 http://dx.doi.org/10.3389/fonc.2021.761700 Text en Copyright © 2021 Wei, Chen, Song, Zhang, Zhang, Xu, Feng, Gao, Qian, Wang, Shang, Zhou, Zhu, Wang, Jia, Liu, Zhu and Li https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms. |
spellingShingle | Oncology Wei, Ling Chen, Jiaxin Song, Chao Zhang, Yuexin Zhang, Yimeng Xu, Mingcong Feng, Chenchen Gao, Yu Qian, Fengcui Wang, Qiuyu Shang, Desi Zhou, Xinyuan Zhu, Jiang Wang, Xiaopeng Jia, Yijie Liu, Jiaqi Zhu, Yanbing Li, Chunquan Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title | Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title_full | Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title_fullStr | Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title_full_unstemmed | Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title_short | Cancer CRC: A Comprehensive Cancer Core Transcriptional Regulatory Circuit Resource and Analysis Platform |
title_sort | cancer crc: a comprehensive cancer core transcriptional regulatory circuit resource and analysis platform |
topic | Oncology |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8546348/ https://www.ncbi.nlm.nih.gov/pubmed/34712617 http://dx.doi.org/10.3389/fonc.2021.761700 |
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