README.md

In patrickCNMartin/ChIPanalyser: ChIPanalyser: Predicting Transcription Factor Binding Sites

ChIPanalyser

ChIPanalyser

ChIPanalyser: Predicting Transcription Factor Binding Sites

Authors

Patrick C.N. Martin [e-mail]

and

Dr. Nicolae Radu Zabet [e-mail]

Description

Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM's) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.

References

Zabet NR, Adryan B (2015) Estimating binding properties of transcription factors from genome-wide binding profiles. Nucleic Acids Res., 43, 84–94.

Patrick C.N. Martin and Nicolae Radu Zabe (2020) Dissecting the binding mechanisms of transcription factors to DNA using a statistical thermodynamics framework. CSBJ, 18, 3590-3605.

patrickCNMartin/ChIPanalyser documentation built on Nov. 24, 2022, 12:02 a.m.