microarray data analysis

Question

[bioinfo]

Hi I have got some common differentially expressed genes. I want to know what all analysis can we do with a particular set of genes and what all features can we get from those genes to make as important for the particular diseases. And also i want to use some classification methods.

Answer 1

[ivivek_ngs]

There are a number of questions that you may answer using your set of DEGs obtained from your analysis. But first google and read some papers upon how to use list of genes differentially expressed between conditions. Google is a good way to start and learn, there will be plenty of hits. In any case some potshots below:

1. Gene Ontology (GO) analysis or in short what are the biological process, cellular locations and molecular functions that are particularly over- or under-represented in your set of genes. Plenty of tools DAVID,Enrichr, etc . Here you get a number of tools and its resources list.

2. What are the pathways that are significantly impacted in your condition? IPA pathway analysis

3. What are the putative mechanisms that could well explain all observed gene expression changes in your system?

4. What are the miRNAs that could be important in this condition based on the gene expression changes observed?

5. You can do Gene Set Enrichment Analysis (GSEA) which determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states (e.g. phenotypes).
6. The association with diseases can be done in Enrichr , as they have different modules that can be run on gene list to get to see how these genes are involved or impacted in other disease phenotypes

I hope all the above information would be good enough for a starting point. Having said that read papers or reviews on Pathway analysis, GO and GSEA or phenotypes relation from list of genes.

[venu]

Adding to the above answer, check this link also

How can I analyze a set of DEGs (differentially expressed genes) to obtain information from them?