Selected article for: "enrichment analysis and functional analysis"
Author: Timothy A. Dinh; Ramja Sritharan; F. Donelson Smith; Adam B. Francisco; Rosanna K. Ma; Rodica P. Bunaciu; Matt Kanke; Charles G. Danko; Andrew P. Massa; John D. Scott; Praveen Sethupathy
Title: Hotspots of aberrant enhancer activity in fibrolamellar carcinoma reveal molecular mechanisms of oncogenesis and intrinsic drug resistance
  • Document date: 2020_1_18
    • ID: bf4qpsy7_62
    Snippet: TRE functional enrichment analysis was performed using GREAT (McLean et al., 2010) . Briefly, TREs were converted from hg38 into hg19 coordinates using the UCSC liftOver tool. GREAT was run using default parameters (whole genome background, basal plus extension association rule). Gene ontology analyses, including KEGG 2016, ARCHS4, and PPI hub enrichment, were performed using Enrichr (Chen et al., 2013) . Windows for enhancer density and gene-enh.....
    Document: TRE functional enrichment analysis was performed using GREAT (McLean et al., 2010) . Briefly, TREs were converted from hg38 into hg19 coordinates using the UCSC liftOver tool. GREAT was run using default parameters (whole genome background, basal plus extension association rule). Gene ontology analyses, including KEGG 2016, ARCHS4, and PPI hub enrichment, were performed using Enrichr (Chen et al., 2013) . Windows for enhancer density and gene-enhancer correlations were defined using gene coordinates based on GENCODE v25 annotations.

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