SPEED2 is a signaling pathway enrichment analysis tool with pathway signatures derived from a large number of manually curated pathway perturbation experiments across many different cell types in human cells. Genes are scored based on causal influences of pathway perturbations as opposed to pathway memberships. Here you can perform an enrichment analysis on a list of human genes against the SPEED2 gene signature database.

For testing you can select an example gene set from the MSigDB Hallmark sets:


Genes to investigate
Paste a list of gene ids (either Entrez Gene IDs or gene symbols (HGNC), separated by space, tabs, line breaks or commas, maximally 500):

Background gene list (optionally)
By default, all genes in the SPEED2 database are background.

Test statistics for enrichment
Bates test (recommended)

Signature genes

Note that the submitted list was tested against the transcriptome-wide ranked gene lists per pathway. In order to extract representative candidates we have also generated gene signatures consisting of the top 300 most significant genes per pathway (provided enough genes were significant). Below you will find the overlap of those signatures with the user-submitted list which you can use to derive representatives for the top regulated pathways. All signature genes can be found on the page Gene signatures

Pathway Gene Regulation Nexp Zrank Pval Qval
Pathway Gene Regulation Nexp Zrank Pval Qval