Importing MSigDB / Finding Measurement Lists or Pathways by keywords.
The Molecular Signatures Database (MSigDB) is a collection of annotated gene sets for use with GSEA software. The MSigDB gene sets are divided into eight major collections;
- Hall mark gene sets, representing well-defined biological states or processes.
- Positional gene sets, representing chromosome and cytoband.
- Curated gene sets, representing online pathways, publications in PubMed, and knowledge of domain experts.
- Motif gene sets, representing conserved cis-regulatory motifs of transcription factors and miRNAs.
- Computational gene sets defined by mining large collections of cancer-oriented microarray data.
- GO gene sets, representing gene annotation of gene ontology terms.
- Oncogenic gene sets defined directly from microarray gene expression data from cancer gene perturbations.
- Immunologic gene sets defined directly from microarray gene expression data from immunologic studies.
Learn more at https://software.broadinstitute.org/gsea/msigdb
You can make use of the gene sets by importing as measurement lists. After that, you can execute the powerful enrichment analysis on them.
"Find Measurement Lists or Pathways tool" is useful to find them from the name or contents gene.
The result table has Redanduncy90 score, which indicates how much redundant the measurement list is. It is the 90th percentile of the number of overlapping measurements against other searching lists. If you want a set of measurement lists which are relatively unique, select lists with the lower Redanduncy90.