GSEA was carried out by using the curated gene sets (C2) of the Molecular Signature Database (MSigDB) version 4.0 provided by the Broad Institute (http://www.broad.mit.edu/gsea/ 55.edu/gsea/ 55
Briefly, genes were univariately screened, and those with a nominal Wilcoxon p < 0.10 were assigned to 1330 known canonical pathways, as defined in the Molecular Signature Database (MSigDB) of Broad Institute19.
Moreover, in CRCs from the TCGA cohort AP4 expression showed a positive correlation with the expression of mRNAs characteristic for Lgr5-positive ISCs14, as well as with mRNAs encoding factors involved in Wnt/β-catenin signaling and c-MYC target genes (mSigDB, molecular signature database:33; Fig. 9b).
Gene sets we used are listed as c2 for curated gene sets in the Molecular Signature Database (MSigDB, http://www.broad.mit.edu/gsea/msigdb/msigdb_index.html).html
This analysis provided insights into the temporal patterns of up- and down-regulation in the gene sets in the Molecular Signature Database (MSigDB) [6].
We used a series of gene sets from the Molecular Signature Database that contains genes grouped based on chromosomal region (c1), pathways (c2) and common motifs (c3).
We downloaded gene annotations from Gene ontology database (http://www.geneontology.org/), and pathway information from two databases, the molecular signature database (MSigDB) and the pathway interaction database (PID).
For GSEA analysis (http://www.broad.mit.edu/gsea/index.jsp), we used the molecular signature database C2, which contains 1892 curated gene sets that are collected from various sources including online pathway databases and knowledge of domain experts.
In addition, the cell cycle and TLR signaling from the collection of canonical pathways (C2 CP) available at the Molecular Signature Database (MSigDb) were enriched in psoriasis lesional skin.
We also performed a Gene Set Enrichment Analysis [48] to find significant overlaps between race/ethnicity-related gene signatures in breast cancer and published signatures archived in the molecular signature database (http://www.broad.mit.edu/gsea/msigdb/).edu/gsea/msigdb/
Curated biological pathway gene sets from the Molecular Signature Database (MsigDB) were screened against the ranked gene list and an order enrichment score (ES) was calculated for each gene set.
