Editing Transcription factor (section)

=== Structural ===

Transcription factors are often classified based on the [[Sequence homology#Homology of sequences in genetics|sequence similarity]] and hence the [[tertiary structure]] of their DNA-binding domains.<ref name="pmid15706513">{{Cite journal |vauthors=Stegmaier P, Kel AE, Wingender E |year=2004 |title=Systematic DNA-binding domain classification of transcription factors |url=http://www.jsbi.org/journal/GIW04/GIW04F028.html |url-status=dead |journal=Genome Informatics. International Conference on Genome Informatics |volume=15 |issue=2 |pages=276–86 |pmid=15706513 |archive-url=https://web.archive.org/web/20130619202726/http://www.jsbi.org/journal/GIW04/GIW04F028.html |archive-date=19 June 2013}}</ref><ref name="Matys_2006">{{Cite journal |vauthors=Matys V, Kel-Margoulis OV, Fricke E, Liebich I, Land S, Barre-Dirrie A, Reuter I, Chekmenev D, Krull M, Hornischer K, Voss N, Stegmaier P, Lewicki-Potapov B, Saxel H, Kel AE, Wingender E |date=January 2006 |title=TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes |journal=Nucleic Acids Research |volume=34 |issue=Database issue |pages=D108-10 |doi=10.1093/nar/gkj143 |pmc=1347505 |pmid=16381825}}</ref><ref>{{Cite web |title=TRANSFAC database |url=http://www.gene-regulation.com/pub/databases/transfac/cl.html |access-date=5 August 2007}}</ref><ref name="Jin_2014" /> The following classification is based of the 3D structure of their [[DNA-binding domain|DBD]] and the way it contacts DNA. It was first developed for Human TF and later extended to rodents <ref name=":0" /> and also to plants.<ref name=":1" /> 
* 1 Superclass: Basic Domains
** 1.1 Class: [[Leucine zipper]] factors ([[bZIP]])
*** 1.1.1 Family: [[AP-1 (transcription factor)|AP-1]](-like) components; includes ([[c-Fos]]/[[c-Jun]])
*** 1.1.2 Family: [[CREB]]
*** 1.1.3 Family: [[Ccaat-enhancer-binding proteins|C/EBP]]-like factors
*** 1.1.4 Family: bZIP / [[PAR (transcription factor)|PAR]]
*** 1.1.5 Family: Plant G-box binding factors
*** 1.1.6 Family: ZIP only
** 1.2 Class: Helix-loop-helix factors ([[bHLH]])
*** 1.2.1 Family: Ubiquitous (class A) factors
*** 1.2.2 Family: Myogenic transcription factors ([[MyoD]])
*** 1.2.3 Family: Achaete-Scute
*** 1.2.4 Family: Tal/Twist/Atonal/Hen
** 1.3 Class: Helix-loop-helix / leucine zipper factors ([[basic helix-loop-helix leucine zipper transcription factors|bHLH-ZIP]])
*** 1.3.1 Family: Ubiquitous bHLH-ZIP factors; includes USF  ([[USF1]], [[USF2]]); SREBP ([[Sterol regulatory element binding protein|SREBP]])
*** 1.3.2 Family: Cell-cycle controlling factors; includes [[Myc|c-Myc]]
** 1.4 Class: NF-1
*** 1.4.1 Family: NF-1  ([[NFIA|A]], [[NFIB (gene)|B]], [[NFIC (gene)|C]], [[NFIX|X]])
** 1.5 Class: RF-X
*** 1.5.1 Family: RF-X ([[RFX1|1]], [[RFX2|2]], [[RFX3|3]], [[RFX4|4]], [[RFX5|5]], [[RFXANK|ANK]])
** 1.6 Class: bHSH
* 2 Superclass: Zinc-coordinating DNA-binding domains
** 2.1 Class: Cys4 [[zinc finger]] of [[nuclear receptor]] type
*** 2.1.1 Family: [[Steroid hormone receptor]]s
*** 2.1.2 Family: [[Thyroid hormone receptor]]-like factors
** 2.2 Class: diverse Cys4 zinc fingers
*** 2.2.1 Family: [[GATA transcription factor|GATA-Factors]]
** 2.3 Class: Cys2His2 zinc finger domain
*** 2.3.1 Family: Ubiquitous factors, includes [[TFIIIA]], [[Sp1 transcription factor|Sp1]]
*** 2.3.2 Family: Developmental / cell cycle regulators; includes [[Krüppel]]
*** 2.3.4 Family: Large factors with NF-6B-like binding properties
** 2.4 Class: Cys6 cysteine-zinc cluster
** 2.5 Class: Zinc fingers of alternating composition
* 3 Superclass: [[Helix-turn-helix]]
** 3.1 Class: [[Homeobox|Homeo domain]]
*** 3.1.1 Family: Homeo domain only; includes [[Ubx]]
*** 3.1.2 Family: [[POU family|POU domain]] factors; includes [[Octamer transcription factor|Oct]]
*** 3.1.3 Family: Homeo domain with LIM region
*** 3.1.4 Family: homeo domain plus zinc finger motifs
** 3.2 Class: Paired box
*** 3.2.1 Family: Paired plus homeo domain
*** 3.2.2 Family: Paired domain only
** 3.3 Class: [[FOX proteins|Fork head]] / [[Winged-helix transcription factors|winged helix]]
*** 3.3.1 Family: Developmental regulators; includes [[forkhead]]
*** 3.3.2 Family: Tissue-specific regulators
*** 3.3.3 Family: Cell-cycle controlling factors
*** 3.3.0 Family: Other regulators
** 3.4 Class: [[Heat Shock Factor]]s
*** 3.4.1 Family: HSF
** 3.5 Class: Tryptophan clusters
*** 3.5.1 Family: Myb
*** 3.5.2 Family: Ets-type
*** 3.5.3 Family: [[Interferon regulatory factors]]
** 3.6 Class: TEA ( transcriptional enhancer factor) domain
*** 3.6.1 Family: TEA ([[TEAD1]], [[TEAD2]], [[TEAD3]], [[TEAD4]])
* 4 Superclass: beta-Scaffold Factors with Minor Groove Contacts
** 4.1 Class: RHR ([[Rel homology domain|Rel homology region]])
*** 4.1.1 Family: Rel/[[Ankyrin repeat|ankyrin]]; [[NF-κB|NF-kappaB]]
*** 4.1.2 Family: ankyrin only
*** 4.1.3 Family: [[NFAT]] ('''N'''uclear '''F'''actor of '''A'''ctivated '''T'''-cells) ([[NFATC1]], [[NFATC2]], [[NFATC3]])
** 4.2 Class: STAT
*** 4.2.1 Family: [[STAT protein|STAT]]
** 4.3 Class: p53
*** 4.3.1 Family: [[p53]]
** 4.4 Class: [[MADS-box|MADS box]]
*** 4.4.1 Family: Regulators of differentiation; includes ([[Mef2]])
*** 4.4.2 Family: Responders to external signals, SRF ([[serum response factor]])  ({{gene|SRF}})
*** 4.4.3 Family: Metabolic regulators (ARG80)
** 4.5 Class: beta-Barrel alpha-helix transcription factors
** 4.6 Class: [[TATA binding protein]]s
*** 4.6.1 Family: TBP
** 4.7 Class: [[HMG-box]]
*** 4.7.1 Family: [[SOX genes]], [[SRY]]
*** 4.7.2 Family: TCF-1 ([[HNF1A|TCF1]])
*** 4.7.3 Family: HMG2-related, [[Structure specific recognition protein 1|SSRP1]]
*** 4.7.4 Family: UBF
*** 4.7.5 Family: MATA
** 4.8 Class: Heteromeric CCAAT factors
*** 4.8.1 Family: Heteromeric CCAAT factors
** 4.9 Class: Grainyhead
*** 4.9.1 Family: Grainyhead
** 4.10 Class: [[Cold-shock domain]] factors
*** 4.10.1 Family: csd
** 4.11 Class: Runt
*** 4.11.1 Family: Runt
* 0 Superclass: Other Transcription Factors
** 0.1 Class: Copper fist proteins
** 0.2 Class: HMGI(Y) ([[HMGA1]])
*** 0.2.1 Family: HMGI(Y)
** 0.3 Class: Pocket domain
** 0.4 Class: E1A-like factors
** 0.5 Class: AP2/EREBP-related factors
*** 0.5.1 Family: [[Apetala 2|AP2]]
*** 0.5.2 Family: EREBP
*** 0.5.3 Superfamily: [[B3 DNA-binding domain|AP2/B3]]
**** 0.5.3.1 Family: ARF
**** 0.5.3.2 Family: ABI
**** 0.5.3.3 Family: RAV