TFARM

The software tool "TFARM" addresses the need to understand genome regulatory networks by focusing on the interactions among transcription factors and chromatin-associated proteins. The motivation stems from these proteins' crucial role in modulating cellular processes, making identifying functional interaction networks a fundamental task. TFARM introduces a novel approach to infer interactions among transcription factors within user-selected genomic regions through association rule computation and a unique Importance Index applied to ChIP-seq datasets. The Importance Index serves as a measure of relevance for the identified interactions among transcription factors. The method's effectiveness is demonstrated through examples of synthetic data, showcasing the utility and potential of the Importance Index. A straightforward pre-processing pipeline facilitates the extraction of input data from any set of ChIP-seq experiments. Applications on ENCODE ChIP-seq data demonstrate the tool's reliability in detecting interactions between transcription factors, including validation with known interactions.