Entering edit mode
7.5 years ago
Chaimaa
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260
Dear all,
I have around 6 sub-networks and their pathway enrichment analysis obtained by DAVID KEGG pathway. I want to understand the exact meaning behind their pathways analysis beside the biological interpretation.
In short, what can i conclude from those pathways?
![https://ibb.co/gb9nfF][1]
Suppose you have a gene list (unregulated / downreg, other criteria?) and you see a lot of genes related to immune system. Now you are wondering if these immune-related genes are there because 1) there are a lot of immune genes in genomes, so they have high probability to be found in any list of similar length. Or 2) they are there because something biologically is triggering the immune response (pathway). The enrichment analysis tries to answer this Q. If there are significantly more immune genes in your list, than could be found by random chance, then it will consider it enriched and consequenctly they might be functionally related to your experiment.
@Santosh Anand, this is exactly what i want to understand. the most set of genes of those 6 subnetworks are sharing some common pathways like Wnt signaling pathway, colorectal cancer, and some other pathways. and so, i want to interpret this findings.
Look individually the annotations of those genes, from say genecards (http://www.genecards.org/). This will help you understand if they are related to some interesting biology of your experiment or just a side-effect of something. Taking forward the immune analogy, a lot of immune related genes are also upregulated when there is any kind of inflammation, and in such cases the immune genes (pathways) will mask the actual trigger of inflammation. If so, you may do the pathway analysis by removing those genes which are masking the analysis. Ultimately, the pathway/GO analysis are just a cue that gives you an idea about the "processes/molecules" important for your biology. How they make sense and fit to your experiment, is really a job you have to figure out as a researcher!
Are you asking about how DAVID does its enrichment analysis ? As far as I know, it's just based on Fisher's exact test and correction for multiple testing. This should be documented somewhere on their web site. It is otherwise unclear what you want to do "beside the biological interpretation". The whole point of doing this kind of analysis is to try and reach some biologically relevant conclusion. However, this needs access to the data and knowledge of the context so we can't do it for you.
Check this article explains about interpretation of enrichment analysis results and what is the reason for performing enrichment analysis.