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Gene Sets from Community ContributorsThis page contains references to gene sets and collections from community contributors. These are not part of MSigDB but may be useful for certain analyses. The descriptions and all other information given below are courtesy of the contributors. Note that these contributions are under copyright and license terms as specified by the authors rather than the MSigDB license terms. If you have gene sets to contribute that might benefit others, either for this page or for inclusion in MSigDB, feel free to contact us at genesets@broadinstitute.org. SysMyo Muscle Gene SetsSysMyo has contributed a collection of Muscle Gene Sets:
"More than ten thousand samples of muscle transcriptomic data have been uploaded to the public Gene
Expression Omnibus in the past ten years, representing many millions of dollars of research expenditure
and incalculable hours of research effort. These data ought to serve as a massive reference set for
ongoing and future studies of neuromuscular disorders. One way to distil the data and render them more
accessible to bench researchers is to extract from each study lists of genes ("gene sets") that were
differentially expressed. With careful curation, each transcriptomic dataset may yield multiple comparisons,
not only relating to the primary focus of that study, such as a pathology or an experimental treatment, but
also more general comparisons not necessarily envisaged by the study's authors, but relating to factors
such as age, sex, and muscle group."
See their website for more information. PorSignDBNicolaas Van Renne et al. have contributed PorSignDB:
"The Porcine Signature Database (PorSignDB) is a collection of annotated gene sets for use with GSEA
software. These gene sets were mostly derived from in vivo derived transcriptomic data, and describe a wide
spectrum of (patho)physiological states of different tissue types. Only a minority of gene sets describe cell
culture systems. Although the original data stems from pigs (Sus Scrofa), gene identifiers were adapted to human
orthologs in order to fit into the MSigDB collection and facilitate its application to data from any mammalian
species..."
See their website for more information. BrainCortex_CellTypeSpecificGenesMegan Hastings Hagenauer et al. have contributed the BrainCortex_CellTypeSpecificGenes gene sets, described in https://www.biorxiv.org/content/early/2017/12/20/089391.full.pdf+html (preprint). From the Abstract:
"Psychiatric illness is unlikely to arise from pathology occurring uniformly across all cell types in
affected brain regions. Despite this, transcriptomic analyses of the human brain have typically been
conducted using macro-dissected tissue due to the difficulty of performing single-cell type analyses with
donated post-mortem brains. To address this issue statistically, we compiled a database of several thousand
transcripts that were specifically-enriched in one of 10 primary cortical cell types, as identified in
previous publications... "
See their website for more information. DSigDBMinjae Yoo et al. have contributed DSigDB, described in https://academic.oup.com/bioinformatics/article/31/18/3069/241009. From the Abstract:
"We report the creation of Drug Signatures Database (DSigDB), a new gene set resource that relates
drugs/compounds and their target genes, for gene set enrichment analysis (GSEA). DSigDB currently holds
22527 gene sets, consists of 17389 unique compounds covering 19531 genes. We also developed an online
DSigDB resource that allows users to search, view and download drugs/compounds and gene sets. DSigDB gene
sets provide seamless integration to GSEA software for linking gene expressions with drugs/compounds for
drug repurposing and translational research. "
See their website for more information. |