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.
For a graphical summary of the idea, see the section Workflow
We also put the paper on bioRxiv, please read all methodological details here: Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF.
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 Bitbucket Issue Tracker. 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, Giovanni Palla, Kasper Dindler Rassmussen, Kristian Helin & Judith B. Zaugg. Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF. 2018. in review
We also put the paper on bioRxiv, please read all methodological details here: Quantification of differential transcription factor activity and multiomic-based classification into activators and repressors: diffTF.
Change log¶
- Version 1.1 (2018-07-27)
- added a new parameter dir_TFBS_sorted in the config file to specify that the TFBS input files are already sorted, which saves some computation time by not resorting them
- updated the TFBS files that are available via download (some files were not presorted correctly)
- added support for single-end BAM files. There is a new parameter pairedEnd in the config file that specifies whether reads are paired-end or not.
- restructured some of the permutation-related output files to save space and computation time. The rule concatenateMotifsPerm should now be much faster, and the TF-specific …outputPerm.tsv.gz files are now much smaller due to an improved column structure
- Version 1.0.1 (2018-07-25)
- fixed a bug in 2.DiffPeaks.R that sometimes caused the step to fail, thanks to Jonas Ungerbeck for letting us know
- fixed a bug in 3.analyzeTF for rare corner cases when DESeq fails
- Version 1.0 (2018-07-01)
- released stable version
License¶
diffTF is licensed under the MIT License:
Copyright (c) 2017 Christian Arnold (carnold@embl.de) & Ivan Berest (berest@embl.de)
Permission is hereby granted, free of charge, to any person obtaining a copy of this software
and associated documentation files (the "Software"), to deal in the Software without
restriction, including without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the
Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or
substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR
PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE
FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
DEALINGS IN THE SOFTWARE.