Gene Set Knowledge Discovery with Enrichr

被引：1819

作者：

Xie, Zhuorui ^{[1
]}

Bailey, Allison ^{[1
]}

Kuleshov, Maxim V. ^{[1
]}

Clarke, Daniel J. B. ^{[1
]}

Evangelista, John E. ^{[1
]}

Jenkins, Sherry L. ^{[1
]}

Lachmann, Alexander ^{[1
]}

Wojciechowicz, Megan L. ^{[1
]}

Kropiwnicki, Eryk ^{[1
]}

Jagodnik, Kathleen M. ^{[1
]}

Jeon, Minji ^{[1
]}

Ma'ayan, Avi ^{[1
]}

机构：

[1] Icahn Sch Med Mt Sinai, Dept Pharmacol Sci, Mt Sinai Ctr Bioinformat, New York, NY 10029 USA

来源：

CURRENT PROTOCOLS | 2021年 / 1卷 / 03期

关键词：

bioinformatics; disease; drug discovery; enrichment analysis; gene sets; visualization; web application; WEB SERVER; EXPRESSION;

D O I：

10.1002/cpz1.90

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (c) 2021 Wiley Periodicals LLC.

引用

页数：51

共 29 条

[1] BABELOMICS:: a systems biology perspective in the functional annotation of genome-scale experiments [J].

Al-Shahrour, Fatima ;

Minguez, Pablo ;

Tarraga, Joaquin ;

Montaner, David ;

Alloza, Eva ;

Vaquerizas, Juan M. ;

Conde, Lucia ;

Blaschke, Christian ;

Vera, Javier ;

Dopazo, Joaquin .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W472-W476

[2] HUMAN GENETICS GTEx pilot quantifies eQTL variation across tissues and individuals [J].

Bahcall, Orli G. .

NATURE REVIEWS GENETICS, 2015, 16 (07) :375-375

[3] D3: Data-Driven Documents [J].

Bostock, Michael ;

Ogievetsky, Vadim ;

Heer, Jeffrey .

IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 2011, 17 (12) :2301-2309

[4] Enrichr: interactive and collaborative HTML']HTML5 gene list enrichment analysis tool [J].

Chen, Edward Y. ;

Tan, Christopher M. ;

Kou, Yan ;

Duan, Qiaonan ;

Wang, Zichen ;

Meirelles, Gabriela Vaz ;

Clark, Neil R. ;

Ma'ayan, Avi .

BMC BIOINFORMATICS, 2013, 14

[5] ToppGene Suite for gene list enrichment analysis and candidate gene prioritization [J].

Chen, Jing ;

Bardes, Eric E. ;

Aronow, Bruce J. ;

Jegga, Anil G. .

NUCLEIC ACIDS RESEARCH, 2009, 37 :W305-W311

[6] Appyters: Turning Jupyter Notebooks into data-driven web apps [J].

Clarke, Daniel J. B. ;

Jeon, Minji ;

Stein, Daniel J. ;

Moiseyev, Nicole ;

Kropiwnicki, Eryk ;

Dai, Charles ;

Xie, Zhuorui ;

Wojciechowicz, Megan L. ;

Litz, Skylar ;

Hom, Jason ;

Evangelista, John Erol ;

Goldman, Lucas ;

Zhang, Serena ;

Yoon, Christine ;

Ahamed, Tahmid ;

Bhuiyan, Samantha ;

Cheng, Minxuan ;

Karam, Julie ;

Jagodnik, Kathleen M. ;

Shu, Ingrid ;

Lachmann, Alexander ;

Ayling, Sam ;

Jenkins, Sherry L. ;

Ma'ayan, Avi .

PATTERNS, 2021, 2 (03)

[7]

Consortium G., 2019, Nucleic Acids Research, V47, P39

[8] GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists [J].

Eden, Eran ;

Navon, Roy ;

Steinfeld, Israel ;

Lipson, Doron ;

Yakhini, Zohar .

BMC BIOINFORMATICS, 2009, 10

[9] Gene Expression Omnibus: NCBI gene expression and hybridization array data repository [J].

Edgar, R ;

Domrachev, M ;

Lash, AE .

NUCLEIC ACIDS RESEARCH, 2002, 30 (01) :207-210

[10] Clustergrammer, a web-based heatmap visualization and analysis tool for high-dimensional biological data [J].

Fernandez, Nicolas F. ;

Gundersen, Gregory W. ;

Rahman, Adeeb ;

Grimes, Mark L. ;

Rikova, Klarisa ;

Hornbeck, Peter ;

Ma'ayan, Avi .

SCIENTIFIC DATA, 2017, 4

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