SLAPE.PATHCOM_HUMAN_nr_i_hu_2014: Collection of pahtway gene-sets from Pathway-Commons (v2014)...

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 and post-processed to reduce their overlaps (see details) and update gene names.

Format

A list containing the following items:

PATHWAY

A string vector in which the i-th entry contains the Pathway-Commons name, or multiple Pathway-Commons name joined (separated by '//'), for the i-th pathway gene-set (or gene-set resulting from merging multiple pathways, see details);

SOURCE

A string vector in which the i-th entry contains the Pathway-Commons description of the source of the i-th pathway, or sources of multiple merged pathways;

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 or multiple merged pathways, differently from SLAPE.PATHCOM_HUMAN_nr_i_hu in this object these symbols are 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;

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.

Details

This object was assembled from a collection of pathway gene sets from the Pathway Commons data portal. From this collection gene sets containing less than 4 genes were discarded. Additionally, in order to remove redundancies those gene sets i) corresponding to the same pathway across different resources or ii) with a large overlap (Jaccard index (J) > 0.8, as detailed below) were merged together by intersecting them. The gene sets resulting from these compressions were then added to the collection (with a joint pathway label) and those participating in at least one of these merging were discarded. The final collection resulting from this pre-processing is composed by 1,636 gene sets, for a total amount of 8,056 unique genes included in at least one gene set. Given two gene sets P_1 and P_2 the corresponding J(P_1,P_2) is defined as:

J(P_1,P_2)=(|P_1 <e2><88><a9> P_2|)/(|P_1 <e2><88><aa> P_2|)

.

Additionally, 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 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/).

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

See Also

SLAPE.PATHCOM_HUMAN, SLAPE.update_HGNC_Table

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