Search
Question: synergy / interaction analysis between gene transcript & correlation / what package to do this ?
0
gravatar for Philippe Guardiola
9.9 years ago by
Philippe Guardiola10 wrote:
Dear R users I would like to have your opinion about the way (and the package that would be able to run this issue) to analyse gene expression data "around transcription factors": there are biological situations in which multiple factors (Transcription factors TF or other cofactors) are involved in the fact that a gene is transcribed, in a way that if TF1 is expressed but not TF2, gene3 is lowly expressed, same if TF2 alone is expressed, and it is only when both TF1 & TF2 are expressed that gene3 is highly expressed. This leads me to think about synergy between TF / interaction term. I d like to explore this in a model we work on in our lab using GEX chips. I was thinking of creating a new variable that would be TF1 signal intensity x TF2 signal intensity and see which gene transcripts correlate with this product term. What is your opinion about such an approach ? Is there a package that would allow me to run this, given the fact that I would like to study all 2x2 interaction terms with the whole set of TF identified on our HT12 illumina chips. As anyone being doing this kind of analysis ? If so should I consider using raw signal of log transformed product term ? Hoping to be not too confused Best wishes for 2009 Regards Philippe Guardiola [[alternative HTML version deleted]]
ADD COMMENTlink written 9.9 years ago by Philippe Guardiola10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 342 users visited in the last hour