New article on arXiv: TF copy number estimation

TF_copy_number_calcWe are very happy to announce the submission of another article to arXiv prior to publication in a peer-reviewed open access journal:

arXiv:1404.5544: Estimating transcription factor abundance and specificity from genome-wide binding profiles

This is a rather curious story, as we had actually been working on something else! If you’re interested in determining the number of bound TF molecules or how to translate PWM scores into actual binding profiles, please have a look, send us comments and suggestions, tweet it, write about it on your blog (but let us know so we can engage in a fruitful scientific discussion!).

In brief, being challenged by the sometimes lengthy compute times of our GRiP framework, Radu Zabet derived an analytical solution for the prediction of genomic occupancy on the basis of TF binding site preference (in the form of a PWM), DNA accessibility (from genome-wide foot printing data), TF copy number and a scaling factor that translates the PWM score into a specificity. However, when benchmarking the method to actual ChIP-seq data, we realised that the same analytical model also allows the inference of TF copy number and specificity if the other two genome-wide measurements (occupancy and DNA accessibility) are given.

This is now an alternative entry point for studies into TF copy numbers, something that our group are also interested in addressing experimentally using quantitative mass-spec.

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