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