I have done an analysis of RNA-seq data using R and uploaded the differentially expressed genes to innateDB. I get that the P-value informs the user of the most likely pathways to be represented by the given data-set. I am just wondering is there any other way to back this up using tools within innateDB or elsewhere? Or is it simply a matter of looking at several pathway summaries and deriving a conclusion from them?
I only came across this question about InnateDB pathway analysis today. Please note that there are some specific issues with RNAseq data that may bias traditional pathway over-representation analyses such as those we implement in InnateDB. These biases are potentially similar to those described for Gene Ontology analysis of RNAseq data (http://genomebiology.com/2010/11/2/R14). I would suggest using GOseq with imported InnateDB pathway annotations for the analysis of RNAseq data. Pathway annotations can easily be obtained from InnateDB by uploading a list of all human/mouse Gene IDs (e.g. from Ensembl) @ http://www.innatedb.com/batchSearchInit.jsp and then choosing to return a list of pathways in the options page.
If you or anyone else have further questions about InnateDB - please contact us directly through innatedb-mail@sfu.ca
I suppose you have a specific reason to use InnateDb, so you are really mostly interested in innate immunity interactions and pathways? In that case is doesn't make much sense to go looking for a better pathway resource. If that is not the case you might want to look at this [?]other question asked today[?] where quite some pathway resources were mentioned.
You could try a standalone pathway statistics procedure on the InnateDb pathways, like a gene set enrichment analysis. But please be aware that your exact statistical procedure for pathway analysis actually is not that relevant. There are so many biological issues (like relevance of a gene to the pathway and the existence of iso-enzymes) that you can not draw strong conclusions from the order of the pathways showing up anyway. It is just a means to decide which pathways to study in more detail.
