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Protocols

MSigDB specifications

Information


Unique identifier OMICS_03995
Name MSigDB
Alternative name Molecular Signatures DataBase
Restrictions to use Academic or non-commercial use
Community driven Yes
Data access File download, Browse
User data submission Not allowed
Version 6.1
Maintained Yes

Taxon


  • Primates
    • Homo sapiens

Maintainer


  • person_outline MSigDB Team

Publications for Molecular Signatures DataBase

MSigDB citations

 (561)
call_split

Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

2018
Nat Commun
PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w
call_split See protocol

[…] es were 15 and 500, respectively at the upper and lower end, and the ‘metric’ used for ranking the genes was the signal-to-noise (S2N). The gene matrix transposed (gmt) file, which was curated by the Molecular Signatures Database (MSigDB) (http://software.broadinstitute.org/gsea/msigdb/) and allows defining the gene sets that are tested for enrichment, is C7-Immunologic Signatures v.5.0; this file […]

library_books

Distinct epigenetic landscapes underlie the pathobiology of pancreatic cancer subtypes

2018
Nat Commun
PMCID: 5958058
PMID: 29773832
DOI: 10.1038/s41467-018-04383-6

[…] Table ) between the siMET basal and scramble basal samples. Fgsea enrichment tests were performed based on Pvalues of the differential analysis of basal siMET vs. basal control samples, and by using MsigDB database and the described open resource. For qPCR, total RNA (1 μg) was used as a template for cDNA synthesis, using the GoScript™ reverse transcription kit (Promega). GoTaq® qPCR 2 × Master M […]

library_books

PCGF5 is required for neural differentiation of embryonic stem cells

2018
Nat Commun
PMCID: 5954019
PMID: 29765032
DOI: 10.1038/s41467-018-03781-0

[…] at least one condition were included. For functional enrichment analysis, all genes were then ranked by log2FC and used in a weighted, pre-ranked GSEA analysis against a collection of gene sets from MSigDB and user defined gene sets by using the neurectoderm and mESC-specific gene lists. Significant associations were determined for any gene set having a FWER p-value below 0.001. […]

call_split

Association between angiogenesis and cytotoxic signatures in the tumor microenvironment of gastric cancer

2018
PMCID: 5953302
PMID: 29785121
DOI: 10.2147/OTT.S162729
call_split See protocol

[…] All gastric cancers analyzed in this study were untreated primary lesions (N = 375). Additional data sets were also downloaded from TCGA in May 2017. The Hallmark gene sets were downloaded from GSEA Molecular Signatures Database v6.0 (http://software.broadinstitute.org/gsea/msigdb/index.jsp). […]

library_books

VAReporter: variant reporter for cancer research of massive parallel sequencing

2018
BMC Genomics
PMCID: 5954270
PMID: 29764369
DOI: 10.1186/s12864-018-4468-5

[…] Pathway component genes are defined as gene sets collected in the Molecular Signatures Database v5.0 (MSigDB) [] that are curated from KEGG [], BioCarta [], Pathway Interaction Database [], Reactome and Signaling Gateway []. VAReporter can assess the mutational even […]

library_books

A genome wide survey of mutations in the Jurkat cell line

2018
BMC Genomics
PMCID: 5941560
PMID: 29739316
DOI: 10.1186/s12864-018-4718-6

[…] re affected than others. The two sets of highly impacted genes were combined, producing a set of 781 unique genes. This list of likely damaged genes was used to probe selected gene set databases from MSigDB []. The top 5 enriched gene sets are displayed in Table . Fig. 5 As might be expected from a cancer cell line, the damaged genes in Jurkat are involved in genome, cell cycle, and cytoskeleton m […]

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MSigDB institution(s)
Broad Institute of MIT and Harvard, Cambridge, MA, USA
MSigDB funding source(s)
Supported by National Cancer Institute, National Institutes of Health, National Institute of General Medical Sciences.

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