myeloma_input

A dataset containing the differentially-expressed genes and adjusted p-values
for the GEO dataset GSE99393. The RNA microarray experiment was perform to
detail the global program of gene expression underlying polarization of
myeloma-associated macrophages by CSF1R antibody treatment. The samples were
6 murine bone marrow derived macrophages co-cultured with myeloma cells
(myeloma-associated macrophages), 3 of which were treated with CSF1R
antibody (treatment group) and the rest were treated with control IgG
antibody (control group). In this dataset, differentially-expressed genes
with |logFC| &gt;= 2 and FDR &lt; 0.05 are presented.
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

myeloma_input function

A data frame with 45 rows and 2 variables:<dl class="dl-horizontal">
 <dt>Gene_Symbol</dt><dd>MGI gene symbols of the differentially-expressed genes</dd>
 <dt>FDR</dt><dd>adjusted p values, via the Benjamini &amp; Hochberg (1995) method</dd>
</dl>

Format

Example Input for Myeloma Analysis (Mus Musculus) — myeloma_input

A data frame with 45 rows and 2 variables:<dl class='dl-horizontal'>
 <dt>Gene_Symbol</dt><dd>MGI gene symbols of the differentially-expressed genes</dd>
 <dt>FDR</dt><dd>adjusted p values, via the Benjamini &amp; Hochberg (1995) method</dd>
</dl>

myeloma_input: Example Input for Myeloma Analysis (Mus Musculus)

Description

Usage

Arguments

Format

See Also