Genome-wide quantification of differential transcription factor activity: diffTF
Summary
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
Documentation
A detailed Documentation is available here:
Installation
First, clone the Github repository:
git clone https://git.embl.de/carnold/diffTF
Follow the steps described in the documentation(https://git.embl.de/carnold/diffTF/blob/master/doc/Documentation.pdf) thereafter.
Instructions to run the example analysis
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Clone the Github repository (see above)
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Change into the example/input directory within the Git repository
cd diffTF/example/input
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Download the data via the download script
sh downloadAllData.sh
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Start a dryrun via the helper script
sh startAnalysis.sh
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Once the dryrun is successful, change the startAnalysis.sh script and remove the dryrun directive to start the analysis and restart the script.
{EDIT THE FILE}sh startAnalysis.sh
Citation
Please cite the following article if you use diffTF in your research:
- Ivan Berest*, Christian Arnold*, Armando Reyes-Palomares, Kasper Rassmussen & Judith B. Zaugg. Genome-wide quantification of differential transcription factor activity: diffTF. 2017. submitted.