GSEA and MSigDB Need Your Support

We are preparing a grant proposal to NCI's Information Technology for Cancer Research program for the continued funding of GSEA and MSigDB. Click here to learn how you can help. (show)

Systematic name M227
Brief description Expressed genes (FPKM>1) associated with high-confidence PAX3-FOXO1 sites with enhancers in primary tumors and cell lines, restricted to those within topological domain boundaries, which are downregulated by delta log2(FPKM) < -0.2
Full description or abstract We identified high-confidence PAX3-FOXO1 target genes by a series of criteria: first, using only PAX3-FOXO1 bound to enhancers recurrent in cell lines and tumors. Secondly, we only selected expressed genes, as PAX3-FOXO1 was not found in repressive chromatin. Third, we excluded nearby expressed genes if they were not found within the same topologically associated domain (TAD) as the PAX3-FOXO1 bound enhancer. Fourth, we also called out the maximally expressed gene within each TAD harboring PAX3-FOXO1. This approach removed 435 nearby but not expressed genes, and 78 expressed but out of TAD bounds. We found 1010 high-confidence targets, 678 of which were novel, and 439 were significantly reduced by shRNA knockdown of PAX3-FOXO1 for 48 hours. The reduced genes are represented in this gene set, which is a subset of GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS.
Collection C2: Curated
      CGP: Chemical and Genetic Perturbations
Source publication Pubmed 28446439   Authors: Gryder BE,Yohe ME,Chou HC,Zhang X,Marques J,Wachtel M,Schaefer B,Sen N,Song Y,Gualtieri A,Pomella S,Rota R,Cleveland A,Wen X,Sindiri S,Wei JS,Barr FG,Das S,Andresson T,Guha R,Lal-Nag M,Ferrer M,Shern JF,Zhao K,Thomas CJ,Khan J
Exact source Supplemental Table 1, tab 2
Related gene sets (show 2 additional gene sets from the source publication)

(show 416 gene sets from the same authors)
External links  
Filtered by similarity ?
Organism Homo sapiens
Contributed by Berkley Gryder (NIH)
Source platform HUMAN_GENE_SYMBOL
Dataset references (show 1 datasets)
Download gene set format: grp | gmt | xml | json | TSV metadata
Compute overlaps ? (show collections to investigate for overlap with this gene set)
Compendia expression profiles ? GTEx compendium
Human tissue compendium (Novartis)
Global Cancer Map (Broad Institute)
NCI-60 cell lines (National Cancer Institute)
Advanced query Further investigate these 438 genes
Gene families ? Categorize these 438 genes by gene family
Show members (show 439 members mapped to 438 genes)
Version history 6.1: First introduced

See MSigDB license terms here. Please note that certain gene sets have special access terms.