We wish to analyze human hiseq transcriptome data sets for differential gene expression in the innate immune pathways modulated by NFkB and metabolic pathways modulated by PPAR-gamma. KEGG is arguably the best public database, but didn't quite help probing deeper into specific pathways. The NIH ImmPort is ok, but clearly too "bulky". I am wondering if anyone has compared these with Ingenuity® Pathway Analysis (IPA®) or can recommend a better database? Thanks!
You have to try GSEA by Broad Institute. This method suites to your goals much better than others. It does not use cut-off thresholds but rather uses all of your data. So, for example if all genes downstream PPAR-gamma are changed 1.4 fold you will not be able to detect this change with traditional method but GSEA will capture this change. It is free online tool and it can run analysis against thousands of gene-sets extracted from literature and many databases, additionally you can create your own datasets based on literature review, your previous experiments etc.
Hi, I worked on both IPA and KEGG and I think KEGG is more efficient!
@Dipankar Ghosh
Hi you can go for a plugin in Cytoscape, ClueGO, and Cluepedia to get your analysis done
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