Pathway Related To Genes Associated For Drought And Salt Stress Tolerance

Question

[Anuraj Nayarisseri]

could you please help me in finding the pathways related to genes responsible for drought and salt stress tolerance.. can you suggest me some pathway db related. Thanks in Advance

Answer 1

[Pierre Lindenbaum]

GOA: http://www.ebi.ac.uk/QuickGO/GSearch?query=salt+stress

Answer 2

[Chris Evelo]

Next thing you could do (after getting the genes from the GO categories that Pierre's search finds) is to use these genes to find gene sets that contain relatively many of those genes in the gene sets that the Broad Institute has collected for GSEA: http://www.broadinstitute.org/gsea/index.jsp. That will find you sets from pathway resources. You could then look up the original (often graphical) pathways at those resources directly.

Answer 3

[Khader Shameer]

Already nice suggestions, I worked (and still working on a similar area) on stress regulome in Arabidopsis thaliana. Here is my thoughts on your question.

IMHO, GO do not capture all of the genes involved in stress-tolerance (or for that matter any given biological process). That is one reason we looked at upregulated genes with respect to various abiotic stress factors including salt in Arabidopsis thaliana from multiple gene expression studies.

We compiled the data of stress responsive genes from Arabidopsis thaliana in STIFDB. Stress Profile of genes influenced by NaCl is available here.

If you go to individual genes, you can see that GO terms associated with these do not mention terms specific to stress or salt but they are perturbed by salt. So, if you need to identify all genes associated with salt tolerance, you should combine genes associated with GO terms with the expression data for salt tolerance in your plant species of interest. Once you have the list of genes you may use WikiPathways or Reactome and perform an enrichment analysis to see statistically significant pathways.

Answer 4

[Larry_Parnell]

This sounds like research in plants and so I checked TAIR and MaizeGDB. The former, for Arabidopsis had nothing for both pathways you seek. MaizeGDB offers more hope, indicating that GO term GO:0009414 - response to water deprivation is a useful GO term on which to parse data. Try this page and this page to get started. I leave other searches up to you. If maize is not your plant of interest, use the proteins thusly annotated as queries to find the homologs/orthologs in your organism.