Question: Innatedb Help Please
gravatar for Bill Stephens
9.8 years ago by
Bill Stephens0 wrote:


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?



ADD COMMENTlink modified 9.5 years ago by David Lynn10 • written 9.8 years ago by Bill Stephens0
gravatar for David Lynn
9.5 years ago by
David Lynn10
David Lynn10 wrote:

Dear Bill,

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 ( 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) @ 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

Regards, David Lynn InnateDB Project Leader.

ADD COMMENTlink written 9.5 years ago by David Lynn10
gravatar for Chris Evelo
9.8 years ago by
Chris Evelo10k
Maastricht, The Netherlands
Chris Evelo10k wrote:

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.

ADD COMMENTlink written 9.8 years ago by Chris Evelo10k
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