RA_input

A dataset containing the differentially-expressed genes along with the
associated (fold-change)
values and FDR adjusted p-values for the GEO dataset GSE15573. This microarray
dataset aimed to characterize gene expression profiles in the peripheral
blood mononuclear cells of 18 rheumatoid arthritis (RA) patients versus 15
healthy subjects. Differentially-expressed genes with adj.P.Val &lt; 0.05 are
presented in this data frame.
Generated on Nov 1, 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_input function

A data frame with 572 rows and 3 variables:<dl class="dl-horizontal">
 <dt>Gene.symbol</dt><dd>HGNC gene symbols of the differentially-expressed genes</dd>
 <dt>logFC</dt><dd>(fold-change) values</dd>
 <dt>adj.P.Val</dt><dd>adjusted p values, via the Benjamini &amp; Hochberg (1995) method</dd>
</dl>

Format

Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis — RA_input

A data frame with 572 rows and 3 variables:<dl class='dl-horizontal'>
 <dt>Gene.symbol</dt><dd>HGNC gene symbols of the differentially-expressed genes</dd>
 <dt>logFC</dt><dd>(fold-change) values</dd>
 <dt>adj.P.Val</dt><dd>adjusted p values, via the Benjamini &amp; Hochberg (1995) method</dd>
</dl>

RA_input: Example Input for the pathfindR Enrichment Workflow - Rheumatoid Arthritis

Description

Usage

Arguments

Format

See Also