TF Info Page for NKX2-8 (Homeodomain)

Conclusion

Assessment Binding Mode Motif Status Notes Comments
Known motif 1 Monomer or homomultimer High-throughput in vitro

Description

Description: NK2 homeobox 8 [Source:HGNC Symbol;Acc:HGNC:16364]
Entrez Summary The protein encoded by this gene is a homeobox-containing developmental regulator associated with liver development. The encoded protein binds to the alpha-fetoprotein (AFP) gene promoter and increases the expression of AFP. This gene is overexpressed in some lung cancers and is linked to poor patient survival, possibly due to its resistance to cisplatin. This gene is aberrantly methylated in pancreatic cancer, deleted in squamous cell lung carcinomas, and acts as a tumor suppressor in esophageal cancer. Mutations in this gene may also be a cause of neural tube defects. [provided by RefSeq, Dec 2015]
Ensembl ID: ENSG00000136327
External Link: CisBP
Interpro IPR001356; IPR009057; IPR017970; IPR020479;
Protein Domain: ENSP00000258829
Domain:
Protein: ENSP00000258829DBD: HomeodomainOther:

Previous Annotations

Source Annotation
TF-CAT classification TF Gene_DNA-Binding
sequence-specific_DNA Binding
Transactivation_
PMIDS:12167706
Vaquerizas 2009 TF classification
"a" Has direct evidence of TF function;
"b" Has evidence for an orthologous TF;
"c" contains likely DBDs, but has no functional evidence;
"x" is an unlikely TF such as predicted gene, genes with likely non-specific DBDs or that have function outside transcription;
"other" category contains proteins without clear DBDs they curated from external sources.
b
CisBP considers it as a TF? Yes
TFclass considers it as a TF? Yes
Has GO:0003700 "transcription factor activity, sequence-specific DNA binding" Yes
GO-Info GO:0001077
RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor a
IDA - PMID:12167706
GO:0003700
sequence-specific DNA binding transcription factor activity
IDA - PMID:9446603
Initial Assessment
1a1 Protein has a high confidence PWM (HT-SELEX, PBM or B1H model) or there is a crystal structure that supports sequence specific DNA binding;
1a2 There is high confidence data for a close ortholog (as defined in CisBP);
2a1 There is lower confidence direct evidence, such as a Jaspar, Hocomoco or Transfac model;
2a2 There is lower confidence evidence for an close ortholog;
3a There is decent circumstantial evidence for its role as a TF or not;
4a Two or more datasets predict it as a TF;
5a One of the source datasets predicts is as a TF
1a1, Direct HQ evidence
TF has conditional DNA-binding requirements

DNA-Binding

Published Motif Data

Source Annotation Motif Evidence
PBMBarrera2016Direct
PBMBarrera2016Direct
HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
Methyl-HT-SELEXYin2017Direct
MiscHocoMocoDirect
PBMBerger08Inferred - Nkx2-9 (96% AA Identity, Mus musculus)
PBMDREAM_contestInferred - Nkx2-9 (96% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx2-2 (91% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-2 (91% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-2 (91% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-2 (91% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX2-2 (91% AA Identity, Homo sapiens)
B1HJASPARInferred - vnd (89% AA Identity, Drosophila melanogaster)
MisciDMMPMMInferred - vnd (89% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - scro (82% AA Identity, Drosophila melanogaster)
PBMBerger06Inferred - ceh-22 (80% AA Identity, Caenorhabditis elegans)
PBMJASPARInferred - ceh-22 (80% AA Identity, Caenorhabditis elegans)
PBMBerger08Inferred - Nkx2-1 (80% AA Identity, Mus musculus)
PBMBerger08Inferred - Nkx2-4 (80% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-1 (80% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (80% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (80% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-1 (80% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX2-1 (80% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-1 (80% AA Identity, Mus musculus)
PBMZoo_01Inferred - ceh-24 (78% AA Identity, Caenorhabditis elegans)
HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-3 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-3 (78% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (78% AA Identity, Homo sapiens)
HT-SELEXYin2017Inferred - NKX2-5 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (78% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX2-5 (78% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-5 (78% AA Identity, Mus musculus)
TransfacTransfacLicense requiredInferred - NKX2-5 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (78% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX2-5 (78% AA Identity, Homo sapiens)
ChIP-seqJASPARInferred - Nkx2-5 (78% AA Identity, Mus musculus)
SELEXJASPARInferred - Nkx2-5 (78% AA Identity, Mus musculus)
MiscHocoMocoInferred - NKX2-5 (78% AA Identity, Homo sapiens)
MiscHOMERInferred - Nkx2-5 (78% AA Identity, Mus musculus)
PBMBarrera2016Inferred - NKX2-5 (77% AA Identity, Homo sapiens)
PBMBarrera2016Inferred - NKX2-5 (77% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx2-6 (75% AA Identity, Mus musculus)
PBMBusserDevelopment2012Inferred - bap (70% AA Identity, Drosophila melanogaster)
B1HJASPARInferred - bap (70% AA Identity, Drosophila melanogaster)
HT-SELEXNitta2015Inferred - bap (70% AA Identity, Drosophila melanogaster)
PBMZoo_01Inferred - bap (70% AA Identity, Drosophila melanogaster)
HT-SELEXYin2017Inferred - NKX3-2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (68% AA Identity, Homo sapiens)
Methyl-HT-SELEXYin2017Inferred - NKX3-2 (68% AA Identity, Homo sapiens)
PBMBerger08Inferred - Nkx3-2 (68% AA Identity, Mus musculus)
SELEXJASPARInferred - NKX3-2 (68% AA Identity, Homo sapiens)
TransfacTransfacLicense requiredInferred - NKX3-2 (68% AA Identity, Homo sapiens)
MiscHocoMocoInferred - NKX3-2 (68% AA Identity, Homo sapiens)

Structure

Structure PDB Not_Covered

Experimental History

Method Constructs
Tried in PBM?
(Whether the protein was tried in PBM or not)
Tried in HT-SELEX
(Whether the protein was tried in HT-SELEX or not, and if so, then what kind of clones were tested)
Other Information?
(Tried with another method and failed?)

External Contribution