Gene Set: GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS

Standard name GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS
Systematic name M157
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
Full description or abstract While previous studies have attempted to identify PAX3-FOXO1 target genes, these were based either on changes in gene expression or proximity to PAX3-FOXO1 in a single cell line with no consideration of expression or chromatin context. By gene expression many targets could be falsely identified which were in fact indirect, and 336 (31%) of the nearby genes previously reported to be direct targets were not expressed, while others may not be physically interacting because of barriers in 3D chromatin space. We therefore 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. Novel targets include 24 oncogenes, 14 pan-cancer upregulated genes, 53 transcription factors, and 7 imprinted genes, many of which were rapidly decommissioned upon depletion of P3F (both reduced RNA-seq and H3K27ac at their enhancers.
Collection C2: curated gene sets
      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
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Organism Homo sapiens
Contributed by Berkley Gryder (NIH)
Source platform HUMAN_GENE_SYMBOL
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Compendia expression profiles Human tissue compendium (Novartis)
NCI-60 cell lines (National Cancer Institute)
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Version history 6.1: First introduced

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