SLAPE.MSigDB_KEGG_hugoUpdated: Collection of KEGG pahtway gene-sets from the Molecular...

In saezlab/SLAPenrich: Sample-population Level Analysis of Pathway enrichments

Description

A list containing KEGG pathway gene-sets downloaded from the Molecular Signature Database (Subramanian et al, 2005) and post-processed to update gene names to recent HUGO nomenclature.

Format

A list containing the following items:

PATHWAY

A string vector in which the i-th entry contains the KEGG pathway name for the i-th pathway gene-set;

SOURCE

A string vector in which the i-th entry contains the source of the i-th pathway;

HGNC_SYMBOL

A list in which the i-th element is a string vector containing the official HUGO symbols of the genes belonging to the i-th pathway or multiple merged pathways, updated to recent nomenclature;

Ngenes

An integer vector in which the i-th element is the number of genes belonging to the i-th pathway;

backGround

A string vector containing the HUGO symbols of all the genes belonging to at least one pathway;

Please note that the name of this list is KEGG_PATH.

Details

All the pathway gene sets contained in this object are updated to recent official HUGO gene nomenclatures, using the informations contained in the SLAPE.hgnc.table data object (which can be itself updated using the dedicated function SLAPE.update_HGNC_Table

Source

This list was assembled from a collection of KEGG pathway gene sets from the Molecular Signature Databse (Subramanian et al, 2005) (http://http://software.broadinstitute.org/gsea/msigdb).

References

Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005 Oct 25;102(43):15545-50

saezlab/SLAPenrich documentation built on May 29, 2019, 12:57 p.m.