Selected article for: "enrichment analysis and GSEA gene set enrichment analysis"
Author: Chang, Stewart T.; Sova, Pavel; Peng, Xinxia; Weiss, Jeffrey; Law, G. Lynn; Palermo, Robert E.; Katze, Michael G.
Title: Next-Generation Sequencing Reveals HIV-1-Mediated Suppression of T Cell Activation and RNA Processing and Regulation of Noncoding RNA Expression in a CD4(+) T Cell Line
  • Document date: 2011_9_20
    • ID: zyzgk2z3_38
    Snippet: DAVID and GSEA analyses. To identify annotations among DE genes, we used the NIH DAVID resource (47, 48) . Default settings were used in DAVID with GO_BP_FAT, GO_CC_FAT, GO_MP_FAT, BIO-CARTA, and KEGG_PATHWAY gene set annotations. Complementary analysis was performed using gene set enrichment analysis (GSEA) (11) . Default settings were used in GSEA with Gene Ontology (GO) categories (c5.all.v2.5 gene sets) and Biocarta and KEGG pathways (c2.all......
    Document: DAVID and GSEA analyses. To identify annotations among DE genes, we used the NIH DAVID resource (47, 48) . Default settings were used in DAVID with GO_BP_FAT, GO_CC_FAT, GO_MP_FAT, BIO-CARTA, and KEGG_PATHWAY gene set annotations. Complementary analysis was performed using gene set enrichment analysis (GSEA) (11) . Default settings were used in GSEA with Gene Ontology (GO) categories (c5.all.v2.5 gene sets) and Biocarta and KEGG pathways (c2.all.v2.5 gene sets) and 5,000 gene set-based permutations. Leading-edge analysis was performed within GSEA to derive genes for hierarchically clustering upand downregulated gene sets.

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