Question: How To Establish A Correlation Between Gene Expression Time-Series And Chip-Chip Data For The Same Time Points?
gravatar for Rayna
9.9 years ago by
Rayna250 wrote:


As the title suggests it, I'd like to correlate two different types of datasets: gene expression and ChIP-chip. Both are time-series, the same organism (E. coli). I don't have a clear idea how to do this, so any suggestion is warmly welcome!

Thanks a lot.

ADD COMMENTlink modified 9.9 years ago by Ian5.7k • written 9.9 years ago by Rayna250
gravatar for Istvan Albert
9.9 years ago by
Istvan Albert ♦♦ 86k
University Park, USA
Istvan Albert ♦♦ 86k wrote:

Start with simple things first.

For example look for correlations between the binding of certain factors and the expression of the genes that are regulated by them. Count all the binding events (x) in a promoter region, then compute the average expression for the regulated genes (y). Do this for each timestep. Now you have two vectors x and y with equal number of values, what is their functional form is, do they correlate at all?

(there will be a fair amount of data shuffling/filtering involved)

With this you can quickly check that your data works at all and that you do indeed have all you need. From this you can then expand on.

ADD COMMENTlink written 9.9 years ago by Istvan Albert ♦♦ 86k
gravatar for Ian
9.9 years ago by
University of Manchester, UK
Ian5.7k wrote:

I have always found the biggest problem of comparing ChIP-chip/seq binding regions with expression data is the use of gene symbols, i.e. whether the genes associated with binding regions also represented in the gene expression data (and visa versa).

So you could simply try intersecting ChIP-chip binding region coordinates (+/-) a threshold of your choice (say 50 or 100kb) with the probeset coordinates from the gene expression data.

For a more in depth and modelled approach i would follow Casey's suggestion.

ADD COMMENTlink written 9.9 years ago by Ian5.7k

Ian brings up an important point that is necessary for the analysis you are interested in doing, how to assign chip hits to target genes: How To Assign A Chip-Chip/Chip-Seq Peak To A Target Gene?

ADD REPLYlink modified 17 months ago by Ram32k • written 9.9 years ago by Casey Bergman18k

Thanks a lot for your ideas and very useful links! I'll check these approaches and give you some feedback :)

Regarding the peak definition, I've come up with a way to do it. I'll answer in the discussion pointed out by Casey.

ADD REPLYlink written 9.9 years ago by Rayna250
gravatar for Casey Bergman
9.9 years ago by
Casey Bergman18k
Athens, GA, USA
Casey Bergman18k wrote:

Rattray, Lawrence, and Sanguinetti have been doing interesting work in this area. You may need to look around to see which of the various methods they have developed suit your needs, but you can try TFinfer for a start, since it is designed for E. coli.

ADD COMMENTlink written 9.9 years ago by Casey Bergman18k
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