MolecularSignaturesDatabase(MSigDB)3.0ArthurLiberzon1,AravindSubramanian1,ReidPinchback1,HelgaThor-aldsdóttir1,PabloTamayo1andJillP.Mesirov1,*1BroadInstitute,Cambridge,MA02142,USA AssociateEditor:DrAlexBateman ABSTRACT Motivation:Well-annotatedgenesetsrepresentingtheuniverseofthebiologicalprocessesarecriticalforme...
Ranked lists were then analyzed for the enrichment of 50 hallmark gene sets (collection H) obtained from the molecular signature database msigDB, maintained by the Broad Institute, using the ‘plotEnrichment’ and ‘plotfgseaRes’ functions in fgsea and the ‘GSEA’ function in DOSE (nperm =...
MSigDB: Molecular Signatures Database MAGEs: Melanoma associated antigens SCGB3A2: Secretoglobin family 3A member 2 ICB: Immune chokepoint inhibitor NKX2-1: NK2 Homeobox 1 TTF-1: Thyroid transcription factor 1 References Haupt S, Caramia F, Klein SL, Rubin JB, Haupt Y. Sex dispar...
Molecular signatures database (MSigDB) 3.0. Bioinformatics. 2011;27:1739–40. Article CAS Google Scholar Wu X, Shukla R, Alganem K, Zhang X, Eby HM, Devine EA, et al. Transcriptional profile of pyramidal neurons in chronic schizophrenia reveals lamina-specific dysfunction of neuronal immunity...
Gene set enrichment analysis (GSEA) was performed, using well-annotated Hallmark gene sets from the Molecular Signatures Database (MSigDB) as input. Principal Component Analysis (PCA) demonstrated a clear segregation of samples into two distinct subgroups (Subgroup_1 and _2). Differential expression...
Development of prognostic signature based on immune-related genes in muscle-invasive bladder cancer: bioinformatics analysis of TCGA database. Aging. 2021;13(2):1859–71. Article CAS PubMed Central PubMed Google Scholar Goldman MJ, Craft B, Hastie M, Repečka K, McDade F, Kamath A, ...
Gene Set Enrichment Analysis MSigDB: Broad Institute Molecular Signature v5 Database miRs: microRNAs References van der Linde D, Konings EE, Slager MA, Witsenburg M, Helbing WA, Takkenberg JJ, et al. Birth prevalence of congenital heart disease worldwide: a systematic review and meta-analys...
For the Xiangya cohort, we calculated the 5mC score directly based on the 5mC gene signature because the survival data of this cohort were not available. Similarly, we calculated the 5mC score directly based on the 5mC gene signature to ensure the comparability of results in the pancancer ...
Therefore, we systematically interrogated 1319 differentially expressed mRNAs (P <0.05) in our dataset [19] using the Molecular Signatures Database (MSigDB) [4]. This led to the identification of enriched microRNA binding motifs, i.e., miR-30, miR-15 and miR-17 (Fig. 1). We then ...
Gene Set Enrichment Analysis (GSEA) was performed with the Molecular Signatures Database (MSigDB) hallmark gene set (Liberzon et al., 2015; Subramanian et al., 2005). Both DESeq2 and MSigDB are provided by the Broad Institute. Quantification and Statistical Analysis All statistical analyses were...