Entering edit mode
5.3 years ago
mlai2567
•
0
Hello all,
I am currently using the GeneMANIA Cytoscape plugin to create network interaction maps based off of my RNA-seq data. I am currently debating if I should include "Gene Interactions," defined by the GeneMANIA FAQ as "functionally associated if the effects of perturbing one gene were found to be modified by perturbations to a second gene," to my figure or if I should just stick to physical interactions.
The basis of my paper is to demonstrate functional relationships between transcriptional events, and was wondering if there was any sort of standard regarding how to present the data.
Thanks in advance! Michael
It all depends on how you define transcriptional events and functional relationships. The latter is usually defined for genes as being involved in the same process for some definition of process. If you define being functionally related as being annotated with the same biological process GO term or being in the same Reactome pathway then it makes sense to include genetic interactions, they are complementary to physical interactions.