By Daniel Himmelstein & Dan Zollinger
Oligodendrocyte precursor cells (OPCs) were recently found to migrate along the vascular endothelium. Here we identify gene pairs that are candidate OPC–endothelial cell interactors. We create a filtered set of gene-gene interactions by:
- filtering for genes that participate in relevant GO terms
- filtering for gene-pairs that exceed an interaction confidence score threshold
- filtering for gene-pairs where one gene is enriched in OPCs and the other is enriched in endothelial cells.
The filtered dataset provides a candidate network of interactions for biologic interrogation.
Execute the notebooks in the following order:
enrichment.ipynb— calculate transcriptional fold changes for OPCs and endothelial cells. Integrate Gene Ontology annotations.interaction.ipynb— integrate protein interactions with expression and GO data. Filter interactions according to user-defined parameters. Create an interaction network.
The following datasets are created:
enrichment.tsv— text file with expression fold changes and GO annotations.filtered.xlsx— spreadsheet with the filtered interactions.network.graphml— network constructed using the filtered interactions. This file can be loaded into Cytoscape 3 using the menu option: File ▶ Import ▶ File.
Expression data is from the Brain RNA-Seq database [Zhang et al (2014) J Neurosci].
Differential expression for Dominant Active-catenin mice was retrieved from a processed version of GSE19403 [Fancy et al (2011) Nat Neurosci].
Protein-protein interactions are extracted from the STRING database version 10 [Szklarczyk et al (2015) Nucl Acids Res].
Gene Ontology annotations are retrieved from user-friendly GO Annotations [Himmelstein et al (2015) Zenodo].
Instructions for biologists:
If you don't already have python, install Anaconda for Python 3.5.
Next clone this repository to your computer. You can also download and extract a zip.
Launch Jupyter (jupyter notebook in terminal or using the Anaconda GUI) and navigate to the opcendo directory.
All original content in this repository is released under CC0 1.0. STRING data is licensed as CC BY 3.0. The Gene Ontology data is licensed as CC BY 4.0. Brain RNA-Seq data is included with permission from its creator Steven Sloan. Data from Fancy et al 2011 is included with permission.