2016 | Maxim V. Kuleshov, Matthew R. Jones, Andrew D. Rouillard, Nicolas F. Fernandez, Qiaonan Duan, Zichen Wang, Simon Koplev, Sherry L. Jenkins, Kathleen M. Jagodnik, Alexander Lachmann, Michael G. McDermott, Caroline D. Monteiro, Gregory W. Gunderson and Avi Ma'ayan
Enrichr is a comprehensive gene set enrichment analysis web server that has been significantly updated. It now contains 180,184 annotated gene sets from 102 gene set libraries. The update includes new features such as the ability to submit fuzzy sets, upload BED files, improved API, and visualization of results as clustergrams. Enrichr is a resource for curated gene sets and a search engine that accumulates biological knowledge for further discoveries. It is freely available at http://amp.pharm.mssm.edu/Enrichr.
The Gene Ontology (GO) was introduced to associate genes with functional biological terms. Early tools like FatiGO, BiNGO, and TermFinder enabled the analysis of gene lists in the context of prior knowledge. Enrichr has been updated with new gene set libraries, including those from HumanCyc, LINCS L1000, NCI-Nature pathways, NURSA, PANTHER, DEPOD, HPO, NIH RePORTER, ENCODE, Allen Brain Atlas, GTEx, ProteomicsDB, and the Achilles Project. These libraries were created through a crowdsourcing project where participants extracted gene expression signatures for specific themes.
Enrichr also includes benchmarking results of different scoring schemes and visualizes the overlap between data sets. The fuzzy enrichment analysis allows for more accurate results by considering gene ranks and magnitudes. Enrichr now supports uploading BED files for genomic region peak analysis and visualizing results as clustergrams. The tool also uses Docker, Mesos, and Marathon for deployment and has a 'Legacy' category for older libraries.
Enrichr has a user-friendly interface and supports various gene set enrichment analysis methods. It is compared with other tools like GO-Elite and MSigDB, showing that Enrichr is more comprehensive. Future directions include adding versions for yeast, worm, and fly, and improving visualization and analysis of user-submitted lists. Enrichr also plans to expand into drug-set enrichment analysis and network-aware methods. The tool is freely available and continues to grow with new libraries and features.Enrichr is a comprehensive gene set enrichment analysis web server that has been significantly updated. It now contains 180,184 annotated gene sets from 102 gene set libraries. The update includes new features such as the ability to submit fuzzy sets, upload BED files, improved API, and visualization of results as clustergrams. Enrichr is a resource for curated gene sets and a search engine that accumulates biological knowledge for further discoveries. It is freely available at http://amp.pharm.mssm.edu/Enrichr.
The Gene Ontology (GO) was introduced to associate genes with functional biological terms. Early tools like FatiGO, BiNGO, and TermFinder enabled the analysis of gene lists in the context of prior knowledge. Enrichr has been updated with new gene set libraries, including those from HumanCyc, LINCS L1000, NCI-Nature pathways, NURSA, PANTHER, DEPOD, HPO, NIH RePORTER, ENCODE, Allen Brain Atlas, GTEx, ProteomicsDB, and the Achilles Project. These libraries were created through a crowdsourcing project where participants extracted gene expression signatures for specific themes.
Enrichr also includes benchmarking results of different scoring schemes and visualizes the overlap between data sets. The fuzzy enrichment analysis allows for more accurate results by considering gene ranks and magnitudes. Enrichr now supports uploading BED files for genomic region peak analysis and visualizing results as clustergrams. The tool also uses Docker, Mesos, and Marathon for deployment and has a 'Legacy' category for older libraries.
Enrichr has a user-friendly interface and supports various gene set enrichment analysis methods. It is compared with other tools like GO-Elite and MSigDB, showing that Enrichr is more comprehensive. Future directions include adding versions for yeast, worm, and fly, and improving visualization and analysis of user-submitted lists. Enrichr also plans to expand into drug-set enrichment analysis and network-aware methods. The tool is freely available and continues to grow with new libraries and features.