scholarly journals Detecting Differential Transcription Factor Activity from ATAC-Seq Data

Molecules ◽  
2018 ◽  
Vol 23 (5) ◽  
pp. 1136 ◽  
Author(s):  
Ignacio Tripodi ◽  
Mary Allen ◽  
Robin Dowell
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Differential Transcription

scholarly journals Detecting differential transcription factor activity from ATAC-seq data

2018 ◽  
Author(s):  
Ignacio J. Tripodi ◽  
Mary A. Allen ◽  
Robin D. Dowell
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Chromatin Accessibility ◽  
Open Chromatin ◽  
Nucleotide Polymorphisms ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Genome Wide ◽  
Recognition Motifs ◽  
Differential Transcription

AbstractTranscription factors are managers of the cellular factory, and key components to many diseases. Many non-coding single nucleotide polymorphisms affect transcription factors, either by directly altering the protein or its functional activity at individual binding sites. Here we first briefly summarize high throughput approaches to studying transcription factor activity. We then demonstrate, using published chromatin accessibility data (specifically ATAC-seq), that the genome wide profile of TF recognition motifs relative to regions of open chromatin can determine the key transcription factor altered by a perturbation. Our method of determining which TF are altered by a perturbation is simple, quick to implement and can be used when biological samples are limited. In the future, we envision this method could be applied to determining which TFs show altered activity in response to a wide variety of drugs and diseases.

scholarly journals Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: DiffTF

2019 ◽  
Author(s):  
Ivan Berest ◽  
Christian Arnold ◽  
Armando Reyes-Palomares ◽  
Giovanni Palla ◽  
Kasper Dindler Rasmussen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Differential Transcription

scholarly journals Quantification of Differential Transcription Factor Activity and Multiomics-Based Classification into Activators and Repressors: diffTF

Cell Reports ◽  
2019 ◽  
Vol 29 (10) ◽  
pp. 3147-3159.e12 ◽  
Author(s):  
Ivan Berest ◽  
Christian Arnold ◽  
Armando Reyes-Palomares ◽  
Giovanni Palla ◽  
Kasper Dindler Rasmussen ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Transcription Factor Activity ◽  
Factor Activity ◽  
Differential Transcription
Sign in / Sign up

Export Citation Format

Share Document