Editing Transcription factor (section)

== Analysis ==

There are different technologies available to analyze transcription factors. On the [[genomic]] level, DNA-[[sequencing]] and database research are commonly used.<ref name="pmid16845064">{{Cite journal |vauthors=Grau J, Ben-Gal I, Posch S, Grosse I |date=July 2006 |title=VOMBAT: prediction of transcription factor binding sites using variable order Bayesian trees |url=http://www.eng.tau.ac.il/~bengal/VOMBAT.pdf |url-status=dead |journal=Nucleic Acids Research |volume=34 |issue=Web Server issue |pages=W529-33 |doi=10.1093/nar/gkl212 |pmc=1538886 |pmid=16845064 |archive-url=https://web.archive.org/web/20180930084306/http://www.eng.tau.ac.il/~bengal/VOMBAT.pdf |archive-date=30 September 2018 |access-date=10 January 2014}}</ref> The protein version of the transcription factor is detectable by using specific [[antibodies]]. The sample is detected on a [[western blot]]. By using [[electrophoretic mobility shift assay]] (EMSA),<ref name="pmid:18591661">{{Cite journal |vauthors=Wenta N, Strauss H, Meyer S, Vinkemeier U |date=July 2008 |title=Tyrosine phosphorylation regulates the partitioning of STAT1 between different dimer conformations |journal=Proceedings of the National Academy of Sciences of the United States of America |volume=105 |issue=27 |pages=9238–43 |bibcode=2008PNAS..105.9238W |doi=10.1073/pnas.0802130105 |pmc=2453697 |pmid=18591661 |doi-access=free}}</ref> the activation profile of transcription factors can be detected. A [[multiplex (assay)|multiplex]] approach for activation profiling is a TF chip system where several different transcription factors can be detected in parallel.{{cn|date=March 2024}}

The most commonly used method for identifying transcription factor binding sites is [[chromatin immunoprecipitation]] (ChIP).<ref>{{Cite journal |vauthors=Furey TS |date=December 2012 |title=ChIP-seq and beyond: new and improved methodologies to detect and characterize protein-DNA interactions |journal=Nature Reviews. Genetics |volume=13 |issue=12 |pages=840–52 |doi=10.1038/nrg3306 |pmc=3591838 |pmid=23090257}}</ref> This technique relies on chemical fixation of chromatin with [[formaldehyde]], followed by co-precipitation of DNA and the transcription factor of interest using an [[antibody]] that specifically targets that protein. The DNA sequences can then be identified by microarray or high-throughput sequencing ([[ChIP-sequencing|ChIP-seq]]) to determine transcription factor binding sites. If no antibody is available for the protein of interest, [[DNA adenine methyltransferase identification|DamID]] may be a convenient alternative.<ref>{{Cite journal |vauthors=Aughey GN, Southall TD |date=January 2016 |title=Dam it's good! DamID profiling of protein-DNA interactions |journal=Wiley Interdisciplinary Reviews: Developmental Biology |volume=5 |issue=1 |pages=25–37 |doi=10.1002/wdev.205 |pmc=4737221 |pmid=26383089}}</ref>