SLAPE.PATHCOM_HUMAN: Collection of pahtway gene-sets from Pathway-Commons

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

Description

A list containing pathway gene-sets from multiple public resources, downloaded from Pathway-Commons.

Format

A list containing the following items:

PATHWAY

A string vector in which the i-th entry contains the Pathway-Commons name of the i-th pathway;

SOURCE

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

UNIPROTID

A list in which the i-th element is a string vector containing the uniprot identifiers of the genes belonging to 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;

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

miniSOURCE

A string vector in which the i-th entry contains the name of the source of the i-th pathway (panther, humancyc, pid or reactome);

includesTP53

A boolean vector whose i-th is TRUE if the i-th pathway contains TP53.

Please note that the name of this list is PATHCOM_HUMAN.

Source

This list was assembled from the collection of pathway gene sets from the Pathway-Commons data portal (v4-201311) (Cerami et al, 2011) (http://www.pathwaycommons.org/archives/PC2/v4-201311/).

References

Cerami EG, Gross BE, Demir E, Rodchenkov I, Babur O, Anwar N, et al. Pathway Commons, a web resource for biological pathway data. Nucleic Acids Res. 2011;39:D685-90

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