network inferring from a course time expression data sets

Question

[zizigolu]

Hi friends,

Supposing I induced the promoter of some transcription factors for example by ethanol. Then expression of genes in my interest plant have been measured in few time points under heat shock. Now how I can infer a network of these expressed genes to understand the involved pathways, key regulator and so on. Do you have any idea please?

Answer 1

[ivivek_ngs]

The only way I can think of here is to find the down stream genes that are being controlled by the transcription factor. Obviously there should be change in the gene expression over time for the those genes that will show difference or variability in the expression for the upstream transcription factor due to its consequences. In that case if you have the time series data and you can plot the DEGs that are coming out of the analysis. You should be able to find the upstream TF for those DEGs. If a TF is a DEG in your analysis or if you have a set of DEGs being controlled by your mentioned TF then any pathway analysis tool like IPA will be able to produce a network of the DEGs that come under the transcription factors and you can infact then control the network construction with String and Cytoscape. For IPA you would need a license to get the full version however the others are free.

[zizigolu]

thank you for your comment