Abstract
Background Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activity of other pathways. Past efforts to identify relationships between biological processes have evaluated overlap in knowledge bases or evaluated changes that occur after specific treatments. Individual experiments can highlight condition-specific pathway-pathway relationships; however, constructing a complete network of such relationships across many conditions requires analyzing results from many studies.
Results We developed PathCORE-T framework by implementing existing methods to identify pathway-pathway transcriptional relationships evident across a broad data compendium. PathCORE-T is applied to the output of feature construction algorithms; it identifies pairs of pathways observed in features more than expected by chance as functionally co-occurring. We demonstrate PathCORE-T by analyzing an existing eADAGE model of a microbial compendium and building and analyzing NMF features from the TCGA dataset of 33 cancer types. The PathCORE-T framework includes a demonstration web interface, with source code, that users can launch to (1) visualize the network and (2) review the expression levels of associated genes in the original data. PathCORE-T creates and displays the network of globally co-occurring pathways based on features observed in a machine learning analysis of gene expression data.
Conclusions The PathCORE-T framework identifies transcriptionally co-occurring pathways from the results of unsupervised analysis of gene expression data and visualizes the relationships between pathways as a network. PathCORE-T recapitulated previously described pathway-pathway relationships and suggested experimentally testable additional hypotheses that remain to be explored.
Footnotes
Co-author e-mail addresses: Kathleen M. Chen: kchen{at}flatironinstitute.org, Jie Tan: tj8901nm{at}gmail.com, Gregory P. Way: gregway{at}mail.med.upenn.edu, Georgia Doing: Georgia.Doing.GR{at}dartmouth.edu, Deborah A. Hogan: Deborah.A.Hogan{at}dartmouth.edu
This manuscript has been updated for clarity and to add the evaluation of a NMF model with fewer dimensions. The references have also been updated to note additional contributions that were submitted after and published before this work was. Also, today I learned that you can put emojis in this field.
