Question: Are Coexpressed Genes In Microarray Expression Data Are Co-Regulated ?
gravatar for khan
7.3 years ago by
khan100 wrote:

Is there any tools to test, whether the set of co-expressed genes in microarray study are also co-regulated or not? I tried ChEA to find the TF of co-expressed genes, but it was not rich database for microRNA.

ADD COMMENTlink modified 2.3 years ago by Biostar ♦♦ 20 • written 7.3 years ago by khan100

As regulation is not just at the level of mRNA, I would do a Gene Ontology [GO] enrichment analysis.

ADD REPLYlink written 7.3 years ago by Alastair Kerr5.3k
gravatar for JC
7.3 years ago by
JC12k wrote:

Answering your biological question, there are some chance of some genes being regulated by the same transcription factors set to be co-expressed, some times this pattern it's very sharp in particular when you expect a non-return control point (like development or cell-specificity). In general this pattern is really noisy, several genes controlled by the same TF barely conserve a co-expression because you know, there are other levels of regulation (transcription rate, mRNA stability, protein modifications, ...). Therefore a lot of strong statistical tests are required and bench validation.

ADD COMMENTlink written 7.3 years ago by JC12k
gravatar for Charles Warden
6.9 years ago by
Charles Warden8.0k
Duarte, CA
Charles Warden8.0k wrote:

I think FIRE is a potentially useful tool because it provides motif and GO enrichment (although it is specifically centered around motifs) for discrete groups:

So, if you define your co-expressed genes as clusters (or using something like k-means clustering), this is meant to address your type of question. I believe it provides both upstream and downstream motifs. There are other similar tools, but this is what I can think of off the top of my head.

ADD COMMENTlink written 6.9 years ago by Charles Warden8.0k
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