Target Genes For Transcription Factors In Plants

Question

[pixie@bioinfo]

I am working on co-expression analysis of rice gene expression data using WGCNA approach. I have obtained a number of gene clusters. I am interested to know whether the transcription factors and their target genes are members of the same cluster or not. The list of TFs have been obtained from the databases but how do I identify their target genes ? TFs are important in crop plants and any ideas on what further studies can be done with the TFs will be greatly appreciated.

[Ashwin]

I would suggest this post on Research gate, A number of online tools are described for identifying target genes for given TF's http://www.researchgate.net/post/How_to_find_the_binding_sites_of_transcription_factors10

Answer 1

[mjoyraj]

Can you please share the script you used for WGCNA approach. Let us say if we have a data set Rdata.csv having 9644 columns (genes) and 15 rows (different time points at which the gene expression is observed) what will be the R script.