Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

2013 | Edward Y Chen, Christopher M Tan, Yan Kou, Qiaonan Duan, Zichen Wang, Gabriela Vaz Meirelles, Neil R Clark and Avi Ma'ayan
Enrichr is an interactive and collaborative web-based and mobile tool for gene list enrichment analysis. It includes new gene-set libraries, a novel method for ranking enriched terms, and various interactive visualizations using the JavaScript library D3. The software can be embedded into other tools that perform gene list analysis. Enrichr was used to analyze nine cancer cell lines by comparing their enrichment signatures to those of matched normal tissues. It revealed common patterns of upregulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interleukin signaling in K562 cells compared to normal myeloid CD33+ cells. These analyses provide a global visualization of critical differences between normal tissues and cancer cell lines. Enrichr provides various types of visualization summaries of collective functions of gene lists. It includes 35 gene-set libraries covering transcription, pathways, ontologies, diseases/drugs, cell types, and miscellaneous. These libraries are created from diverse sources, including databases like ChEA, TRANSFAC, JASPAR, ENCODE, and others. Enrichr computes enrichment using three methods: Fisher exact test, a correction to the Fisher exact test based on expected rank deviation, and a combined score. It also provides visualization options such as bar graphs, tables, grids, and networks to display enrichment results. Enrichr is open source and freely available online at http://amp.pharm.mssm.edu/Enrichr. It is accessible via web and mobile applications, and users can share results, export figures, and store their lists. Enrichr is easy to use and provides a comprehensive tool for gene set enrichment analysis, with a user-friendly interface and various visualization options. It is suitable for a wide range of applications, including cancer research, and can be integrated into RNA-seq pipelines. The tool is supported by NIH grants and is available for use on various platforms, including desktop and mobile devices.Enrichr is an interactive and collaborative web-based and mobile tool for gene list enrichment analysis. It includes new gene-set libraries, a novel method for ranking enriched terms, and various interactive visualizations using the JavaScript library D3. The software can be embedded into other tools that perform gene list analysis. Enrichr was used to analyze nine cancer cell lines by comparing their enrichment signatures to those of matched normal tissues. It revealed common patterns of upregulation of the polycomb group PRC2 and enrichment for the histone mark H3K27me3 in many cancer cell lines, as well as alterations in Toll-like receptor and interleukin signaling in K562 cells compared to normal myeloid CD33+ cells. These analyses provide a global visualization of critical differences between normal tissues and cancer cell lines. Enrichr provides various types of visualization summaries of collective functions of gene lists. It includes 35 gene-set libraries covering transcription, pathways, ontologies, diseases/drugs, cell types, and miscellaneous. These libraries are created from diverse sources, including databases like ChEA, TRANSFAC, JASPAR, ENCODE, and others. Enrichr computes enrichment using three methods: Fisher exact test, a correction to the Fisher exact test based on expected rank deviation, and a combined score. It also provides visualization options such as bar graphs, tables, grids, and networks to display enrichment results. Enrichr is open source and freely available online at http://amp.pharm.mssm.edu/Enrichr. It is accessible via web and mobile applications, and users can share results, export figures, and store their lists. Enrichr is easy to use and provides a comprehensive tool for gene set enrichment analysis, with a user-friendly interface and various visualization options. It is suitable for a wide range of applications, including cancer research, and can be integrated into RNA-seq pipelines. The tool is supported by NIH grants and is available for use on various platforms, including desktop and mobile devices.
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