Biological motivation

Transcription factor (TF) activity constitutes an important readout of cellular signalling pathways and thus for assessing regulatory differences across conditions. However, current technologies lack the ability to simultaneously assessing activity changes for multiple TFs and surprisingly little is known about whether a TF acts as repressor or activator. To this end, we introduce the widely applicable genome-wide method diffTF to assess differential TF binding activity and classifying TFs as activator or repressor by integrating any type of genome-wide chromatin with RNA-Seq data and in-silico predicted TF binding sites

Help, contribute and contact

If you have questions or comments, feel free to contact us. We will be happy to answer any questions related to this project as well as questions related to the software implementation. For method-related questions, contact Judith B. Zaugg (judith.zaugg@embl.de) or Ivan Berest (berest@embl.de). For technical questions, contact Christian Arnold (christian.arnold@embl.de).

If you have questions, doubts, ideas or problems, please use the Issue Tracker at https://git.embl.de/grp-zaugg/diffTF/issues. We will respond in a timely manner.

Citation

If you use this software, please cite the following reference: Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.

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