The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets.Results: We report the availability of a new version of the database, MSigDB 3.0, with over 6700 gene sets, a complete revision of the collection of canonical pathways and experimental ...
msigdbsignaturesdatabasemoleculargenesets 1MolecularSignaturesDatabase(MSigDB)3.0ArthurLiberzon1,AravindSubramanian1,ReidPinchback1,HelgaThor-valdsdóttir1,PabloTamayo1andJillP.Mesirov1,*1BroadInstitute,Cambridge,MA02142,USAABSTRACTMotivation:Well-annotatedgenesetsrepresentingtheuniverseofthebiologicalprocessesarecri...
Title An R Package for Exploring Molecular Signatures Database Version1.0 Description The Molecular Signatures Database('MSigDB')is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis<doi:10.1016/j.cels.2015.12.004>.The'msig'package ...
Motivation: Well-annotated gene sets representing the universe of the biological processes are critical for meaningful and insightful interpretation of large-scale genomic data. The Molecular Signatures Database (MSigDB) is one of the most widely used repositories of such sets. Results: We report the...
TheMolecular Signatures Database (MSigDB)in a tidy data frame. This is the updated version of the archived repo of@stephenturner Current version:v2023.2.Hs(Oct 2023). Installation #Install devtools if you don't already have itinstall.packages("devtools")#Just get the datadevtools::install_gith...
For this analysis, we selected the so-called hallmark collection of gene sets from the Molecular Signatures Database (MSigDB), since it concisely summarizes a diverse set of biological processes27. We computed the mean gNAS and gFib scores of DEGs (1% FDR) in each significantly regulated ...
(d) using the Molecular Signatures Database (MSigDB) C1 collection between HER2-0 (N = 61) and HER2-low (N = 355) breast cancers.Pvalues were computed using a two-sided Fisher’s exact test. The centerline represents the median, the box limits represent the upper and lower ...
The molecular signatures database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1:417–25. https://doi.org/10.1016/j.cels.2015.12.004. Article CAS Google Scholar Ashburner M, et al. Gene ontology: tool for the unification of biology. Nat Genet. 2000;25:25–9. https://doi....
The Molecular Signatures Database (MSigDB) hallmark gene set collection. Cell Syst. 2015;1(6):417–25. Article CAS PubMed PubMed Central Google Scholar Ye Y, Hu Q, Chen H, Liang K, Yuan Y, Xiang Y, et al. Characterization of hypoxia-associated molecular features to aid hypoxia-...
Molecular signatures database (MSigDB) 3.0 Bioinformatics, 27 (2011), pp. 1739-1740 Crossref View in Scopus Google Scholar 20 J. Liu, T. Lichtenberg, K.A. Hoadley, L.M. Poisson, A.J. Lazar, A.D. Cherniack, A.J. Kovatich, C.C. Benz,et al. ...