I'm looking for tools that would allow me to integrate and interrogate 3 datasets generated from the same samples: mRNA and miRNA expression from Affymetrix arrays, plus LC-MS/MS relative protein abundance from a 6-plex TMT dataset. Each sample has 3 biological replicates.
If you've done this kind of analysis before, please comment on approaches that work well, as well as approaches to avoid. Thanks!
You might want to try PathVisio (see www.pathvisio.org). That will definitely work for proteomics and mRNA data. It can in principle support miRNA data. But the problem likely is that there are not too many miRNA's in existing pathways. We usually use Cytoscape for that part. You can use the GPML Cytoscape plugin to get PathVisio/WikiPathways pathways in Cytoscape and then use e.g. CyTargetLinker to add miRNA's and use a visalization plugin for your data on top of that.
Dear Chris, thank you for the advice. Do you know a nice tool to integrate all these 3 platforms :proteomics (DIGE-MS), transcriptomics (RNA seq) and metabolomics (GC-MS) data?
Does anyone have a good suggestion?
Combine the three data sets to one big matrix and use the fabia algorithm (http://www.bioconductor.org/packages/release/bioc/html/fabia.html ) to extract some biclusters.
Worked fine on miRNA and mRNA...
- Badges
- Science topic
- Similar topics
- Bioinformatics
- Bioinformatics and Computational Biology