Question: Are Coexpressed Genes In Microarray Expression Data Are Co-Regulated ?
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gravatar for khan
6.2 years ago by
khan100
Germany
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 13 months ago by Biostar ♦♦ 20 • written 6.2 years ago by khan100

As regulation is not just at the level of mRNA, I would do a Gene Ontology [GO] enrichment analysis. http://www.geneontology.org/GO.tools.shtml

ADD REPLYlink written 6.2 years ago by Alastair Kerr5.2k
1
gravatar for JC
6.2 years ago by
JC9.1k
Mexico
JC9.1k 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 6.2 years ago by JC9.1k
1
gravatar for Charles Warden
5.7 years ago by
Charles Warden7.3k
Duarte, CA
Charles Warden7.3k 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:

https://tavazoielab.c2b2.columbia.edu/FIRE/

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 5.7 years ago by Charles Warden7.3k
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