Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks

Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Her...

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Detalles Bibliográficos
Autores principales: Li, Shaojuan, Wan, Changxin, Zheng, Rongbin, Fan, Jingyu, Dong, Xin, Meyer, Clifford A, Liu, X Shirley
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2019
Materias:
Web Server Issue
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602521/
https://www.ncbi.nlm.nih.gov/pubmed/31053864
http://dx.doi.org/10.1093/nar/gkz332
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author Li, Shaojuan
Wan, Changxin
Zheng, Rongbin
Fan, Jingyu
Dong, Xin
Meyer, Clifford A
Liu, X Shirley
author_facet Li, Shaojuan
Wan, Changxin
Zheng, Rongbin
Fan, Jingyu
Dong, Xin
Meyer, Clifford A
Liu, X Shirley
author_sort Li, Shaojuan
collection PubMed
description Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/.
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spelling pubmed-66025212019-07-05 Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks Li, Shaojuan Wan, Changxin Zheng, Rongbin Fan, Jingyu Dong, Xin Meyer, Clifford A Liu, X Shirley Nucleic Acids Res Web Server Issue Characterizing the ontologies of genes directly regulated by a transcription factor (TF), can help to elucidate the TF’s biological role. Previously, we developed a widely used method, BETA, to integrate TF ChIP-seq peaks with differential gene expression (DGE) data to infer direct target genes. Here, we provide Cistrome-GO, a website implementation of this method with enhanced features to conduct ontology analyses of gene regulation by TFs in human and mouse. Cistrome-GO has two working modes: solo mode for ChIP-seq peak analysis; and ensemble mode, which integrates ChIP-seq peaks with DGE data. Cistrome-GO is freely available at http://go.cistrome.org/. Oxford University Press 2019-07-02 2019-05-04 /pmc/articles/PMC6602521/ /pubmed/31053864 http://dx.doi.org/10.1093/nar/gkz332 Text en © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Web Server Issue
Li, Shaojuan
Wan, Changxin
Zheng, Rongbin
Fan, Jingyu
Dong, Xin
Meyer, Clifford A
Liu, X Shirley
Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title_full Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title_fullStr Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title_full_unstemmed Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title_short Cistrome-GO: a web server for functional enrichment analysis of transcription factor ChIP-seq peaks
title_sort cistrome-go: a web server for functional enrichment analysis of transcription factor chip-seq peaks
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6602521/
https://www.ncbi.nlm.nih.gov/pubmed/31053864
http://dx.doi.org/10.1093/nar/gkz332
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