Question: KEGG Cancer Pathway
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gravatar for bioinformatics.cancer
2.4 years ago by
United States
bioinformatics.cancer180 wrote:

Hi, I have used KEGG for pathway analysis for a gene expression data set and one of the pathways that comes up enriched is the "Pathways in Cancer" (hsa05200). This is a very generic pathway with many components. The diagram shows several processes within the pathway such as "Metastasis", "Evading Apoptosis", "Proliferation" etc. I am trying to figure out how to interpret such a broad pathway definition. My interest is mainly in understanding if "Metastasis" pathway is enriched in my data set. I would appreciate any help with interpreting "Pathways in Cancer". Thanks, - Pankaj

cancer kegg pathway • 1.1k views
ADD COMMENTlink modified 2.4 years ago by Jean-Karim Heriche20k • written 2.4 years ago by bioinformatics.cancer180
0
gravatar for Jean-Karim Heriche
2.4 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche20k wrote:

I don't know how you've done the analysis but you could test at a higher level of granularity i.e. test if individual pathways forming the "pathways in cancer" group are enriched. It could be that one or two of these pathways give the signal you detected. Alternatively, it could be that no pathway is individually enriched and given the broad scope of this Pathways in cancer, I'd be careful about not putting too much into this result. I don't think KEGG has any pathway specifically labelled as metastasis, it is an end-point of several pathways. What you could also do is look for biological process GO terms enrichment and see if there's any sign of processes associated with metastasis e.g. cell movement or microtubule-based movement and their descendants.

ADD COMMENTlink written 2.4 years ago by Jean-Karim Heriche20k
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