Question: Mining condition specific gene expression data
gravatar for Arun
5.0 years ago by
Arun2.3k wrote:


tl;dr version - How can we use Genevestigator to find out if the set of genes we've obtained from DGE analysis of our RNA-Seq data specific to a condition (biotic stress) are also induced in response to various other biotic stresses or not? We work with the model plant Arabidopsis thaliana.


We've done a differential expression analysis on a RNA-Seq data (control - condition type) and obtained a set of genes (within a gene family) that are induced (and highly represented) under this biotic stress. Now what we'd like to check is if the same set of genes are also induced under various other biotic stress compared to the other genes within the gene family. If not, it could strengthen the hypothesis that these genes are more likely to be induced due to this particular stress condition.

Ideally, we'd like to obtain a list of genes known to be induced under various biotic stress, from leaf samples under the same developmental stages from our RNA-Seq experiment. By comparing this with the one from RNA-Seq data (using Fisher's test), we should be able to test this hypothesis.

Any pointers on how to go about mining for this using Genevesitgator would be really helpful. Also, would a pro-version be required to obtain this data? 

Thank you.



rna-seq microarray data-mining • 1.2k views
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