string_adj_list

An adjacency list of vectors containing interactors B for each interactor A
in the STRING protein-protein interaction network (The designations
"interactor A" and "interactor B" are arbitrary). Only interactions with a combined
score &gt;= 800 were kept.
Generated on Oct 31, 2019.

datasets

Enrichment analysis enables researchers to uncover mechanisms
underlying a phenotype. However, conventional methods for enrichment
analysis do not take into account protein-protein interaction information,
resulting in incomplete conclusions. pathfindR is a tool for enrichment
analysis utilizing active subnetworks. The main function identifies active
subnetworks in a protein-protein interaction network using a user-provided
list of genes and associated p values. It then performs enrichment analyses
on the identified subnetworks, identifying enriched terms (i.e. pathways or,
more broadly, gene sets) that possibly underlie the phenotype of interest.
pathfindR also offers functionalities to cluster the enriched terms and
identify representative terms in each cluster, to score the enriched terms
per sample and to visualize analysis results. The enrichment, clustering and
other methods implemented in pathfindR are described in detail in
Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for
Comprehensive Identification of Enriched Pathways in Omics Data Through
Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>.

Ege Ulgen

pathfindR

Enrichment Analysis Utilizing Active Subnetworks

Ozan Ozisik

string_adj_list function

list containing 11934 vectors. Each vector is the set of gene symbols
of interactors B for each interactor A.

string_adj_list: STRING PIN Adjacency List

Description

Usage

Arguments

Format