Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

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 Gundersen, Avi Ma'ayan, 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 Gundersen, Avi Ma'ayan

Abstract

Enrichment analysis is a popular method for analyzing gene sets generated by genome-wide experiments. Here we present a significant update to one of the tools in this domain called Enrichr. Enrichr currently contains a large collection of diverse gene set libraries available for analysis and download. In total, Enrichr currently contains 180 184 annotated gene sets from 102 gene set libraries. New features have been added to Enrichr including the ability to submit fuzzy sets, upload BED files, improved application programming interface and visualization of the results as clustergrams. Overall, Enrichr is a comprehensive resource for curated gene sets and a search engine that accumulates biological knowledge for further biological discoveries. Enrichr is freely available at: http://amp.pharm.mssm.edu/Enrichr.

© The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Figures

Figure 1.
Figure 1.
Benchmarking different enrichment analysis methods. (A) Deviation of the cumulative distribution from uniform of the scaled ranks of TFs derived from different enrichment analysis methods; (B) Comparison between crisp and fuzzy version of the proportion test. The ranking distribution of randomly ordered ChEA terms is plotted in gray dashed line. The area under the curve (AUC) is indicated in the legend as a measure of the degree of deviation from uniform.
Figure 2.
Figure 2.
Statistics of Enrichr. (A) Histogram of gene lists submitted per user. (B) Histogram of uploaded list lengths. (C) Histogram of appearance of genes in uploaded list. (D) Histogram of annotated gene set sizes within Enrichr.
Figure 3.
Figure 3.
Comparing Enrichr resources with MSigDB and GO-Elite. (A) Venn diagram summarizing the various resources processed and served by Enrichr, MSigDB and GO-Elite. (B) Venn diagram to compare the number of processed gene sets of genetic and chemical perturbations curated from publications in Enrichr and MSigDB.

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