Dear all,
I have two questions.
Q1: How do I load and analyse my metabolomics data?
I have metabolomics data of ~170 metabolites. These metabolites have been measured in Hela cells in a control group and a treatment group over a time series. So, I have in total 11 different groups of samples (in triplicate): 0 hour control and 2 hour control, 2 hour treatment, 4h control, 4h treatment ... up until 10 hours. My question is how do I load this data in cytoscape? Do I need to normalize the peak areas prior to loading in cytoscape? And can I load all my groups at once, or do I have to load my data separately? And how would I analyse these different groups in cytoscape?
Q2: Can I analyse metabolomics and proteomics data in combination in cytoscape, and if yes, how?
In addition to the metabolomics data, I also have proteomics data. I would like to analyse these two datasets together. The proteomics dataset has only one control group (so, not per timepoint as is the case for the metabolomics dataset) and is already log2 transformed, but is otherwhise similar to the metabolomics dataset (treatment groups at 2,4,6,8,10 hours in triplicate). Is it possible to analyse the metabolomics and proteomics data set together in cytoscape? And if yes, again how do I load and analyse the data? And if not, is there another program/option to analyse both datasets together?
Yours sincerely, Lonneke Nouwen
Well, it depends on what you want to do with Cytoscape, could you provide more info on that? Cytoscape is dedicated to network analysis. A classical analysis is to find relevant pathways by loading a metabolic network first and then import your data to map them onto the network. Your metabolites must have been identified and use the same identifier system than your network. There is dedicated plugins for this kind of analysis, see MetScape for example that can be of interest to you: http://metscape.ncibi.org/ If not, another solution to map both metabolomics and proteomics data is MetExplore (https://metexplore.toulouse.inra.fr), again, it depends on what you want to do. (Disclamer: though not directly involved in MetExplore development I'm part of the same group)
You'll still need to harmonize identifiers (MetScape use KEGG ones), the chemical translation service can help you do that : https://cts.fiehnlab.ucdavis.edu/