FishEnrichr

Input data

Choose an input file to upload. Either in BED format or a list of genes. For a quantitative set, add a comma and the level of membership of that gene. The membership level is a number between 0.0 and 1.0 to represent a weight for each gene, where the weight of 0.0 will completely discard the gene from the enrichment analysis and the weight of 1.0 is the maximum.

Or paste in a list of gene symbols optionally followed by a comma and levels of membership. Try two examples: crisp set example, fuzzy set example

0 gene(s) entered

Enter a brief description for the list in case you want to share it. (Optional)

Contribute

Please acknowledge FishEnrichr in your publications by citing the following references:
Chen EY, Tan CM, Kou Y, Duan Q, Wang Z, Meirelles GV, Clark NR, Ma'ayan A. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics. 2013;128(14).

Kuleshov MV, Jones MR, Rouillard AD, Fernandez NF, Duan Q, Wang Z, Koplev S, Jenkins SL, Jagodnik KM, Lachmann A, McDermott MG, Monteiro CD, Gundersen GW, Ma'ayan A. Enrichr: a comprehensive gene set enrichment analysis web server 2016 update. Nucleic Acids Research. 2016; gkw377 .

Announcing FishEnrichr a part of the new ModEnrichr toolkit - August 1, 2018

FishEnrichr is a new gene list enrichment analysis tool for Danio rerio. FishEnrichr is derived from Enrichr, the popular web-based software for comprehensive and intuitive gene list enrichment analysis. Data from a variety of publicly available D. rerio databases was processed and integrated to generate a collection of gene set libraries. FishEnrichr can be accessed via API which are documented in SmartAPI. This makes FishEnrichr interoperable with other tools and projects.

The initial version of FishEnrichr contain the following new gene set libraries:

Gene Ontology: The GO libraries were created using the core ontology from the Gene Ontology Consortium, annotated with associated D. rerio genes. A cross-section of the ontology tree was taken to create moderately sized gene sets. The three gene set libraries in FishEnrichr are: GO Biological Process, GO Cellular Component, and GO Molecular Function.

WikiPathways: The WikiPathways library consists of all pathways for D. rerio in WikiPathways converted to gene sets.
Coexpression Predicted: Libraries were created using gene-gene expression correlations built from gene counts in GEO and SRA fish experiments, based on a methodology developed in ARCHS4. The average correlation of a gene to all the genes currently associated with a term is calculated, scaled using zscore, and the top 200 genes with scores greater than 1.95 are predicted to be associated with the term. The three libraries in FishEnrichr are: Coexpression Predicted GO BP, Coexpression Predicted GO MF, and Coexpression Predicted GO CC.

Developed	in	the Ma'ayan Lab
	by	Edward Chen
		Maxim Kuleshov
		Zachary Flamholz
		Matthew Jones
		Christopher Tan
		Yan Kou
		Neil Clark
		Andrew Rouillard
		Nick Fernandez
		Qiaonan Duan
		Zichen Wang
		Simon Koplev
		Sherry Jenkins
		Alexander Lachmann
		Michael McDermott
		Caroline Monteiro
		Gregory Gundersen
		Avi Ma'ayan

modEnrichr	Enrichr	FlyEnrichr	YeastEnrichr	WormEnrichr
A suite of gene list enrichment analysis tools	Enrichr	FlyEnrichr	YeastEnrichr	WormEnrichr