Question: How to identify transcription factors (TFs) from expression data comparison?
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gravatar for XC
3.3 years ago by
XC20
Germany
XC20 wrote:

Dear All,

I have a dataset of gene expression which consists two kinds of cells: 5 replicates of testing vs 5 replicates of controlling. Is there any tools / web-based platforms which can generate TFs based on the differentially expressed genes between testing group and controlling group? For example, if I have a differentially expressed gene list between testing group and controlling group, may I find reliable TFs which result in the behavior of testing group? Then I can validate them experimentally.

Thank you very much.

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ADD COMMENTlink modified 3.2 years ago by Gian350 • written 3.3 years ago by XC20

I don't think this experiment design is suitable for detecting TF's. You will likely get more reliable predictions based on sequence similarity.

ADD REPLYlink written 3.3 years ago by Michael Dondrup45k

Hi Michael, thank you very much for your suggestions. Right, based on sequence data we can get more reliable predictions, but now I only have microarray data with oligo probes, that's why I have to find solution based on the differentially expressed gene list.

ADD REPLYlink written 3.3 years ago by XC20
0
gravatar for Gian
3.2 years ago by
Gian350
Canada
Gian350 wrote:

Are these human cell lines? If you are interested in identifying TFs that might regulate a differentially expressed gene you can calculate the correlation between the expression profile of your gene and a list of TFs. Considering that the expression profile only includes 10 samples you probably would then want to confirm a similar strong correlation( or anticorrelation if TF is a negative regulator) in other expression dataset and look for predicted TFBS close to the genomic coordinates of your gene of interest.

ADD COMMENTlink written 3.2 years ago by Gian350

Hi Gian, thank you very much. Right, these are human cell lines. Your suggestion is great and meaningful. 

ADD REPLYlink written 3.1 years ago by XC20
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