pathways


  There are 572,639 pathways and their component genes downloaded from collection 2 and collection 5 of MSigDB (http://www.broadinstitute.org/gsea/msigdb/index.jsp).


MSigDB

Elucidation of human disease similarities has emerged as an active research area, which is highly relevant to etiology, disease classification, and drug repositioning. This package was designed and implemented for identifying disease similarities. It contains five functions which are 'DCEA', 'DCpathway', 'DS', 'comDCGL' and 'comDCGLplot'. In 'DCEA' function, differentially co-expressed genes and differentially co-expressed links are extracted from disease vs. health samples. Then 'DCpathway' function assigns differential co-expression values of pathways to be the average differential co-expression value of their component genes. Then 'DS' employs partial correlation coefficient of pathways as the disease similarity for each disease pairs. And 'DS' contains a permutation process for evaluating the statistical significant of observed disease partial correlation coefficients. At last, 'comDCGL' and 'comDCGLplot' sort out shared differentially co-expressed genes and differentially co-expressed links with regulation information and visualize them.

Jing Yang

DSviaDRM

Exploring Disease Similarity in Terms of Dysfunctional
Regulatory Mechanisms

pathways function

A data frame with 572,639 observations 2 variables.
<ul>
<li>pathways A data frame with 572,639 observations 2 columns. TF-to-target interaction pairs. 
</li>
</ul> 

pathways: The dataset of human pathways downloaded from two collections of MSigDB

Description

Usage

Arguments

Format

Details

Examples