Gene Set Knowledge Discovery with Enrichr

Zhuorui Xie; Allison Bailey; Maxim V. Kuleshov; Daniel J.B. Clarke; John E. Evangelista; Sherry L. Jenkins; Alexander Lachmann; Megan L. Wojciechowicz; Eryk Kropiwnicki; Kathleen M. Jagodnik; Minji Jeon; Avi Ma'ayan

doi:10.1002/cpz1.90

Gene Set Knowledge Discovery with Enrichr

Zhuorui Xie, Allison Bailey, Maxim V. Kuleshov, Daniel J.B. Clarke, John E. Evangelista, Sherry L. Jenkins, Alexander Lachmann, Megan L. Wojciechowicz, Eryk Kropiwnicki, Kathleen M. Jagodnik, Minji Jeon, Avi Ma'ayan

Research output: Contribution to journal › Article › peer-review

1310 Scopus citations

Abstract

Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high-profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website.

Original language	English
Article number	e90
Journal	Current Protocols
Volume	1
Issue number	3
DOIs	https://doi.org/10.1002/cpz1.90
State	Published - Mar 2021

Keywords

bioinformatics
disease
drug discovery
enrichment analysis
gene sets
visualization
web application

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10.1002/cpz1.90

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title = "Gene Set Knowledge Discovery with Enrichr",

abstract = "Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high-profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website.",

keywords = "bioinformatics, disease, drug discovery, enrichment analysis, gene sets, visualization, web application",

author = "Zhuorui Xie and Allison Bailey and Kuleshov, {Maxim V.} and Clarke, {Daniel J.B.} and Evangelista, {John E.} and Jenkins, {Sherry L.} and Alexander Lachmann and Wojciechowicz, {Megan L.} and Eryk Kropiwnicki and Jagodnik, {Kathleen M.} and Minji Jeon and Avi Ma'ayan",

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year = "2021",

month = mar,

doi = "10.1002/cpz1.90",

language = "English",

volume = "1",

journal = "Current Protocols",

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AU - Clarke, Daniel J.B.

AU - Evangelista, John E.

AU - Jenkins, Sherry L.

AU - Lachmann, Alexander

AU - Wojciechowicz, Megan L.

AU - Kropiwnicki, Eryk

AU - Jagodnik, Kathleen M.

AU - Jeon, Minji

AU - Ma'ayan, Avi

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AB - Profiling samples from patients, tissues, and cells with genomics, transcriptomics, epigenomics, proteomics, and metabolomics ultimately produces lists of genes and proteins that need to be further analyzed and integrated in the context of known biology. Enrichr (Chen et al., 2013; Kuleshov et al., 2016) is a gene set search engine that enables the querying of hundreds of thousands of annotated gene sets. Enrichr uniquely integrates knowledge from many high-profile projects to provide synthesized information about mammalian genes and gene sets. The platform provides various methods to compute gene set enrichment, and the results are visualized in several interactive ways. This protocol provides a summary of the key features of Enrichr, which include using Enrichr programmatically and embedding an Enrichr button on any website.

KW - bioinformatics

KW - disease

KW - drug discovery

KW - enrichment analysis

KW - gene sets

KW - visualization

KW - web application

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JF - Current Protocols

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ER -

Gene Set Knowledge Discovery with Enrichr

Abstract

Keywords

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