RA_exp_mat

A matrix containing the -transformed
and quantile-normalized expression values of the differentially-expressed
genes for 18 rheumatoid arthritis (RA) patients and 15 healthy subjects. The
matrix contains expression values of 572 significantly
differentially-expressed genes (see <code><a rd-options="" href="/link/RA_input?package=pathfindR&version=1.4.2" data-mini-rdoc="pathfindR::RA_input">RA_input</a></code>) with adj.P.Val &lt;= 0.05.
Generated on Sep 28, 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

RA_exp_mat function

A matrix with 572 rows and 33 columns.

Format

A matrix containing the -transformed
and quantile-normalized expression values of the differentially-expressed
genes for 18 rheumatoid arthritis (RA) patients and 15 healthy subjects. The
matrix contains expression values of 572 significantly
differentially-expressed genes (see <code><a rd-options='' href='RA_input'>RA_input</a></code>) with adj.P.Val &lt;= 0.05.
Generated on Sep 28, 2019.

RA_exp_mat: Example Input for pathfindR - Enriched Term Scoring

Description

Usage

Arguments

Format

See Also