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CRdb: a comprehensive resource for deciphering chromatin regulators in human

Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to...

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Autores principales: Zhang, Yimeng, Zhang, Yuexin, Song, Chao, Zhao, Xilong, Ai, Bo, Wang, Yuezhu, Zhou, Liwei, Zhu, Jiang, Feng, Chenchen, Xu, Liyan, Wang, Qiuyu, Sun, Hong, Fang, Qiaoli, Xu, Xiaozheng, Li, Enmin, Li, Chunquan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825595/
https://www.ncbi.nlm.nih.gov/pubmed/36318256
http://dx.doi.org/10.1093/nar/gkac960
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author Zhang, Yimeng
Zhang, Yuexin
Song, Chao
Zhao, Xilong
Ai, Bo
Wang, Yuezhu
Zhou, Liwei
Zhu, Jiang
Feng, Chenchen
Xu, Liyan
Wang, Qiuyu
Sun, Hong
Fang, Qiaoli
Xu, Xiaozheng
Li, Enmin
Li, Chunquan
author_facet Zhang, Yimeng
Zhang, Yuexin
Song, Chao
Zhao, Xilong
Ai, Bo
Wang, Yuezhu
Zhou, Liwei
Zhu, Jiang
Feng, Chenchen
Xu, Liyan
Wang, Qiuyu
Sun, Hong
Fang, Qiaoli
Xu, Xiaozheng
Li, Enmin
Li, Chunquan
author_sort Zhang, Yimeng
collection PubMed
description Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes.
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spelling pubmed-98255952023-01-10 CRdb: a comprehensive resource for deciphering chromatin regulators in human Zhang, Yimeng Zhang, Yuexin Song, Chao Zhao, Xilong Ai, Bo Wang, Yuezhu Zhou, Liwei Zhu, Jiang Feng, Chenchen Xu, Liyan Wang, Qiuyu Sun, Hong Fang, Qiaoli Xu, Xiaozheng Li, Enmin Li, Chunquan Nucleic Acids Res Database Issue Chromatin regulators (CRs) regulate epigenetic patterns on a partial or global scale, playing a critical role in affecting multi-target gene expression. As chromatin immunoprecipitation sequencing (ChIP-seq) data associated with CRs are rapidly accumulating, a comprehensive resource of CRs needs to be built urgently for collecting, integrating, and processing these data, which can provide abundant annotated information on CR upstream and downstream regulatory analyses as well as CR-related analysis functions. This study established an integrative CR resource, named CRdb (http://cr.liclab.net/crdb/), with the aim of curating a large number of available resources for CRs and providing extensive annotations and analyses of CRs to help biological researchers clarify the regulation mechanism and function of CRs. The CRdb database comprised a total of 647 CRs and 2,591 ChIP-seq samples from more than 300 human tissues and cell types. These samples have been manually curated from NCBI GEO/SRA and ENCODE. Importantly, CRdb provided the abundant and detailed genetic annotations in CR-binding regions based on ChIP-seq. Furthermore, CRdb supported various functional annotations and upstream regulatory information on CRs. In particular, it embedded four types of CR regulatory analyses: CR gene set enrichment, CR-binding genomic region annotation, CR-TF co-occupancy analysis, and CR regulatory axis analysis. CRdb is a useful and powerful resource that can help in exploring the potential functions of CRs and their regulatory mechanism in diseases and biological processes. Oxford University Press 2022-11-01 /pmc/articles/PMC9825595/ /pubmed/36318256 http://dx.doi.org/10.1093/nar/gkac960 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Nucleic Acids Research. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Database Issue
Zhang, Yimeng
Zhang, Yuexin
Song, Chao
Zhao, Xilong
Ai, Bo
Wang, Yuezhu
Zhou, Liwei
Zhu, Jiang
Feng, Chenchen
Xu, Liyan
Wang, Qiuyu
Sun, Hong
Fang, Qiaoli
Xu, Xiaozheng
Li, Enmin
Li, Chunquan
CRdb: a comprehensive resource for deciphering chromatin regulators in human
title CRdb: a comprehensive resource for deciphering chromatin regulators in human
title_full CRdb: a comprehensive resource for deciphering chromatin regulators in human
title_fullStr CRdb: a comprehensive resource for deciphering chromatin regulators in human
title_full_unstemmed CRdb: a comprehensive resource for deciphering chromatin regulators in human
title_short CRdb: a comprehensive resource for deciphering chromatin regulators in human
title_sort crdb: a comprehensive resource for deciphering chromatin regulators in human
topic Database Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9825595/
https://www.ncbi.nlm.nih.gov/pubmed/36318256
http://dx.doi.org/10.1093/nar/gkac960
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