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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Veröffentlicht in:	Nucleic acids research Jg. 47; H. W1; S. W212 - W224
Hauptverfasser:	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
Format:	Journal Article
Sprache:	Englisch
Veröffentlicht:	England Oxford University Press 02.07.2019
Schlagworte:	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
Online-Zugang:	Volltext
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Abstract	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.
AbstractList	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. 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.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.
Author	Keenan, Alexandra B Jagodnik, Kathleen M Lachmann, Alexander Wojciechowicz, Megan L Kropiwnicki, Eryk Wang, Zichen Leong, Ariel K Ma’ayan, Avi Torre, Denis Utti, Vivian
AuthorAffiliation	Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
AuthorAffiliation_xml	– name: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
Author_xml	– sequence: 1 givenname: Alexandra B surname: Keenan fullname: Keenan, Alexandra B organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 2 givenname: Denis surname: Torre fullname: Torre, Denis organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 3 givenname: Alexander surname: Lachmann fullname: Lachmann, Alexander organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 4 givenname: Ariel K surname: Leong fullname: Leong, Ariel K organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 5 givenname: Megan L surname: Wojciechowicz fullname: Wojciechowicz, Megan L organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 6 givenname: Vivian surname: Utti fullname: Utti, Vivian organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 7 givenname: Kathleen M orcidid: 0000-0002-2755-2097 surname: Jagodnik fullname: Jagodnik, Kathleen M organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 8 givenname: Eryk surname: Kropiwnicki fullname: Kropiwnicki, Eryk organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 9 givenname: Zichen orcidid: 0000-0002-1415-1286 surname: Wang fullname: Wang, Zichen organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA – sequence: 10 givenname: Avi orcidid: 0000-0002-6904-1017 surname: Ma’ayan fullname: Ma’ayan, Avi organization: Department of Pharmacological Sciences, Mount Sinai Center for Bioinformatics, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1603, New York, NY 10029, USA
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/31114921$$D View this record in MEDLINE/PubMed
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Snippet	Identifying the transcription factors (TFs) responsible for observed changes in gene expression is an important step in understanding gene regulatory networks....
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SubjectTerms	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
Title	ChEA3: transcription factor enrichment analysis by orthogonal omics integration
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