RA_input

A dataset containing the differentially-expressed genes along with the
associated log2-fold-change values and adjusted p-values for the GEO dataset
GSE15573. The 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 dataset.

datasets

Pathway enrichment analysis enables researchers to uncover mechanisms
underlying the phenotype. pathfindR is a tool for pathway enrichment analysis
utilizing active subnetworks. It identifies active subnetworks in a
protein-protein interaction network using user-provided a list of genes.
It performs pathway enrichment analyses on the identified subnetworks.
pathfindR also offers functionalities to cluster enriched pathways and identify
representative pathways and to score the pathways per sample. The method is
described in detail in Ulgen E, Ozisik O, Sezerman OU. 2018. pathfindR: An R
Package for Pathway Enrichment Analysis Utilizing Active Subnetworks. bioRxiv.
<doi:10.1101/272450>.

Ege Ulgen

pathfindR

Pathway Enrichment Analysis Utilizing Active Subnetworks

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>log2-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>log2-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