I looked everywhere on the net but I'm unable to answer these questions.
I have a dataset from a microarray experiment (>50 000 probesets, observed throught 4 times and 5 patients)
I made a clustering of the gene expression. I further want to make a gene regulatory inference.
But to do so, I want to incorporate biological prior information. But I need to now :
- the potential TFs of each of my clusters (based, for example on a TFBS enrichment analysis)
- the potential targets of each TF in my whole gene selection
I would like to find a tool to make both of my taks. I need them to be in R (R-bioconductor).
I read JASPAR with TFBStools may be a good strating point. But I really don't understand how to start : with the list of the genes, with the promoter sequence of the genes (if yes, how can I get these sequences ?)...
Is there something in R like oPOSSUM, that allows to analyse in a direct way a list of genes ?
Thank you in advance, I'm a little lost.