ChEA3: transcription factor enrichment analysis by orthogonal omics integration

Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene s...

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Vydáno v:Nucleic acids research Ročník 47; číslo W1; s. W212 - W224
Hlavní autoři: Keenan, Alexandra B, Torre, Denis, Lachmann, Alexander, Leong, Ariel K, Wojciechowicz, Megan L, Utti, Vivian, Jagodnik, Kathleen M, Kropiwnicki, Eryk, Wang, Zichen, Ma’ayan, Avi
Médium: Journal Article
Jazyk:angličtina
Vydáno: England Oxford University Press 02.07.2019
Témata:
Chromatin Immunoprecipitation Sequencing - methods
Computational Biology - methods
Databases, Genetic
Datasets as Topic
Gene Expression Regulation - genetics
Gene Library
Gene Regulatory Networks - genetics
Humans
Transcription Factors - genetics
Web Server Issue
ISSN:0305-1048, 1362-4962, 1362-4962
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Popis
Shrnutí:Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks. ChIP-X Enrichment Analysis 3 (ChEA3) is a transcription factor enrichment analysis tool that ranks TFs associated with user-submitted gene sets. The ChEA3 background database contains a collection of gene set libraries generated from multiple sources including TF–gene co-expression from RNA-seq studies, TF–target associations from ChIP-seq experiments, and TF–gene co-occurrence computed from crowd-submitted gene lists. Enrichment results from these distinct sources are integrated to generate a composite rank that improves the prediction of the correct upstream TF compared to ranks produced by individual libraries. We compare ChEA3 with existing TF prediction tools and show that ChEA3 performs better. By integrating the ChEA3 libraries, we illuminate general transcription factor properties such as whether the TF behaves as an activator or a repressor. The ChEA3 web-server is available from https://amp.pharm.mssm.edu/ChEA3.
Bibliografie:ObjectType-Article-1
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkz446