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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
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.
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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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