ID
stringlengths 10
16
| Name
stringlengths 1
14
| DBD
stringclasses 75
values | Is TF?
stringclasses 2
values | TF assessment
stringclasses 5
values | Binding mode
stringclasses 4
values | Motif status
stringclasses 4
values | Notes
stringclasses 11
values | Comments
stringlengths 10
585
⌀ | Committee notes
stringclasses 79
values | MTW Notes
stringclasses 44
values | TRH Notes
stringclasses 96
values | SL notes
stringclasses 35
values | AJ notes
stringclasses 124
values | Disagree on Assessment
stringclasses 1
value | Disagree on Binding
stringclasses 1
value | Author1
stringclasses 7
values | Assesment1
stringclasses 5
values | Binding1
stringclasses 4
values | Comment1
stringlengths 3
401
⌀ | Notes1
stringclasses 161
values | Author2
stringclasses 8
values | Assesment2
stringclasses 5
values | Binding2
stringclasses 6
values | Comment2
stringlengths 3
502
⌀ | Notes2
stringclasses 61
values | Vaquerizas 2009 TF classification
stringclasses 7
values | CisBP considers it as a TF?
stringclasses 3
values | TFclass considers it as a TF?
stringclasses 2
values | TF-CAT classification
stringlengths 1
200
⌀ | Is a GO TF
stringclasses 3
values | PDB
stringclasses 208
values |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
ENSG00000137203
|
TFAP2A
|
AP-2
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:11522791;15475956
|
Yes
| null |
ENSG00000008196
|
TFAP2B
|
AP-2
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Matt Weirauch
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:7555706
|
Yes
| null |
ENSG00000087510
|
TFAP2C
|
AP-2
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Matt Weirauch
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000008197
|
TFAP2D
|
AP-2
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
|
Binds the same GCCTGAGGC sequence as the other AP-2s (PMID: 24789576)
| null | null | null | null |
Binds the same GCCTGAGGC sequence as the other AP-2:s based on PMID: 24789576
|
Disagree
| null |
Arttu Jolma
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
Binds GCCTGAGGC sequence based on PMID: 24789576
| null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Source of Hocomoco motif is unclear
| null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000116819
|
TFAP2E
|
AP-2
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:14572467
|
Yes
| null |
ENSG00000117713
|
ARID1A
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null |
Non-specific DNA binder (PMID: 15170388).
| null | null | null | null | null | null | null |
Matt Weirauch
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
non-specific DNA binder: PMID 15170388
| null |
Pratyush Das
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Pubmed: 10757798
| null | null | null | null | null | null | null |
ENSG00000049618
|
ARID1B
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null |
Non-specific DNA binder (PMID: 15170388).
| null | null | null | null | null |
Disagree
|
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
ARID domain and full-length should be tested
|
Matt Weirauch
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null | null |
No
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding; DNA-Binding: non-sequence-specific; Transcription Regulatory Activity: heterochromatin interaction/binding_TF PPI_PMIDS:12200431;15170388
|
No
| null |
ENSG00000116017
|
ARID3A
|
ARID/BRIGHT
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
| null | null |
100% DBDID to mouse, which has PBM
| null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
The lower confidence models seem legit; similar AT-rich motif as those observed for paralogs using PBM
| null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
other
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:15456761
|
Yes
| null |
ENSG00000179361
|
ARID3B
|
ARID/BRIGHT
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null |
Disagree
| null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Factor Binding: tf co-factor binding; DNA-Binding: non-sequence-specific_DNA Binding; TF PPI_PMIDS:10446990
|
Yes
| null |
ENSG00000205143
|
ARID3C
|
ARID/BRIGHT
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null |
Disagree
| null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
|
There is unpublished HT-SELEX data for ARID3C
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
Indeterminate - There is no evidence for or against this genes role as a TF__Other_PMIDS:15922553
|
Yes
| null |
ENSG00000032219
|
ARID4A
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
|
Has a putative AT-hook
|
Binds DNA in a sequence non-specific manner (PMID: 15640446).
| null | null | null | null | null | null |
Disagree
|
Tim Hughes
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
Only the ARID3 and ARID5 subclasses are sequence specific
| null |
Yimeng Yin
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
It binds to DNA in a sequence non-specific manner. [PMID: 15640446]
| null |
No
|
Yes
|
Yes
|
TF Gene_Transcription Regulatory Activity: heterochromatin interaction/binding; Transcription Factor Binding: tf co-factor binding_Other; TF PPI_PMIDS:10321733;10490602
|
Yes
| null |
ENSG00000054267
|
ARID4B
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null |
Binds DNA in a sequence non-specific manner (PMID: 15640446).
| null | null | null | null | null |
Disagree
|
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
ARID domain and full-length should be tested
|
Yimeng Yin
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
See ARID4A for evidence
| null |
No
|
Yes
|
Yes
|
TF Gene_Transcription Regulatory Activity: heterochromatin interaction/binding_Co-activation; TF PPI_PMIDS:12724404
|
No
| null |
ENSG00000196843
|
ARID5A
|
ARID/BRIGHT
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Indirect motif has 100% DBD Identity to mouse Arid5a (PBM motif)
| null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
Indeterminate - There is no evidence for or against this genes role as a TF___PMIDS:0
|
No
| null |
ENSG00000150347
|
ARID5B
|
ARID/BRIGHT
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
|
Has a putative AT-hook
| null |
100% DBDID to mouse, which has PBM
| null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
crystal structure PDB: 2OEH is with dsDNA TACAATATAACGTCG
| null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
other
|
Yes
|
Yes
|
TF Gene Candidate_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:8649988;10329386
|
Yes
|
2OEH
|
ENSG00000008083
|
JARID2
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null |
Only ARID3 and ARID5 family members have sequence specificity (PMID: 15640446).
| null | null | null | null | null |
Disagree
| null |
Tim Hughes
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Only ARID3 and ARID5 family members have sequence specificity (PMID:15640446)
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
PMID: 12890668
| null |
No
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000073614
|
KDM5A
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null | null | null | null | null | null | null |
Disagree
| null |
Jussi Taipale
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null |
ARID domain and full-length should be tested
|
Sam Lambert
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
KDM5A is a known transcriptional co-factor
| null |
No
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding_Co-activation; TF PPI_PMIDS:9129143;11358960;15949438
|
Yes
| null |
ENSG00000117139
|
KDM5B
|
ARID/BRIGHT
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null |
Binds GC-rich sequences such as CCGCCC (PMID: 18270511).
| null | null | null | null | null | null | null |
Arttu Jolma
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
Has been shown to be a histone de-methylase that operates as a transcriptional cofactor; could however have innate sequence specificity due to presence of a ARID-domain
| null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
Prefer to GC-rich sequence; such as CCGCCC [PMID: 18270511]
| null |
No
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding_TF PPI; Transactivation_PMIDS:12657635
|
Yes
| null |
ENSG00000126012
|
KDM5C
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null | null | null | null | null | null | null | null |
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
ARID domain; check for residues required for DNA binding
|
Arttu Jolma
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Has low-specificity ARID-domain and histone demethylase activity besides chromatin recognition domain PHD
| null |
No
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Regulatory Activity: heterochromatin interaction/binding_Other_PMIDS:17320160
|
No
| null |
ENSG00000012817
|
KDM5D
|
ARID/BRIGHT
|
No
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
No motif
| null |
Polycomb protein that is well-documented to bind histone marks (PMID: 27477906; PMID: 17351630; PMID: 17320160; PMID: 17320162).
| null | null | null | null | null |
Disagree
|
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
ARID domain and full-length should be tested
|
Laura Campitelli
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
Polycomb protein that is well-documented to bind histone marks [PMID: 27477906; PMID: 17351630; PMID: 17320160; PMID: 17320162]
| null |
No
|
Yes
|
Yes
|
Indeterminate - There is no evidence for or against this genes role as a TF___PMIDS:0
|
No
| null |
ENSG00000189079
|
ARID2
|
ARID/BRIGHT; RFX
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
ARID domain; check for residues required for DNA binding
|
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
x
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding_Co-activation_PMIDS:16782067
|
No
| null |
ENSG00000153207
|
AHCTF1
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null |
Disagree
| null |
Jussi Taipale
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null |
name says AT-hook; but domain not called; should be checked
|
Laura Campitelli
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Recruits nucleoporins to chromatin [PMID: 17235358]
|
Should not be initial assessment 1a1?
|
c
|
No
|
No
|
No
|
No
| null |
ENSG00000126705
|
AHDC1
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
AT-Hook domains are only picked up by SMART domain searches. There is no experimental evidence to suggest it binds DNA or functions as a TF.
| null |
Laura Campitelli
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null | null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000106948
|
AKNA
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null |
Binds AT-rich promoters of CD40 and CD40L and coordinates their expression (PMID: 11268217).
| null | null | null | null | null |
Disagree
|
Disagree
|
Tim Hughes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
11268217 claims it binds DNA; but there is no motif as yet.
| null |
Laura Campitelli
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Debatable - binds AT-rich promoters of CD40 and CD40L and coordinates their expression; but likely doesn't bind a specific sequence [PMID: 11268217]
|
Debatable - binds AT-rich promoters of CD40 and CD40L and coordinates their expression; but likely doesn't bind a specific sequence [PMID: 11268217]
|
c
|
No
|
No
|
No
|
Yes
| null |
ENSG00000116539
|
ASH1L
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
Protein is a histone methyltransferase PMID: 17923682
| null |
Pratyush Das
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
a
|
No
|
No
|
No
|
No
| null |
ENSG00000173894
|
CBX2
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null |
Has single SMART AT hook
| null | null | null |
Disagree
|
Disagree
|
Sam Lambert
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
Yimeng Yin
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
AT-hook containing protein
| null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000101457
|
DNTTIP1
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
|
Has a putative AT-hook
| null | null | null | null | null | null |
Disagree
|
Disagree
|
Arttu Jolma
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
PMID:11473582 Terminal deoxynucleotidyltransferase (TdT) is a DNA polymerase that enhances Ig and TcR gene diversity in the N region in B- and T-cells.
| null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
No
|
No
|
No
|
No
| null |
ENSG00000104885
|
DOT1L
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null |
Disagree
| null |
Arttu Jolma
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Protein is a histone methyltransferase; has a putative AT-hook GRKRGRPKKMN and could thus have low specificity interactions with DNA
| null |
Yimeng Yin
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Two databases claimed this proteins contains a putative AT-hook.
| null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000140632
|
GLYR1
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
|
Has a putative AT-hook
| null | null | null | null | null | null |
Disagree
|
Disagree
|
Laura Campitelli
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
Binds histones [PMID: 20850016]
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
AT hook type needs reconsideration; UniProtKB - Q49A26
|
AT hook type DNA binding
|
x
|
No
|
No
|
No
|
No
| null |
ENSG00000137309
|
HMGA1
|
AT hook
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
| null |
Reannotated as AT Hook
| null | null | null |
Name is misleading, it does not have a HMG domain but three AT-hooks
| null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null |
Has also HMG DBDs
|
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
|
We've obtained motif for it in the new data.
| null |
c
|
Yes
|
Yes
|
TF Gene_DNA-Binding: non-sequence-specific; Transcription Factor Binding: tf co-factor binding_DNA Binding_PMIDS:9199299;12907668
|
Yes
|
2EZD
|
ENSG00000149948
|
HMGA2
|
AT hook
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
| null | null |
100% DBDID to mouse, which has PBM
| null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
Binds DNA specifically based on PMID:14627817. Transfac and Hocomoco models are probably correct in vivo sites
| null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
x
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000025293
|
PHF20
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null |
HAT complex member (PMID 27760318). Does contain possible AT-hook
| null | null | null |
Disagree
| null |
Arttu Jolma
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Protein is a component of histone acetyl-transferase complex that recognises H3K4me2 to add H4K16ac modification PMID:27760318. Has potential AT-hook KRKR-GRP-PSIA
| null |
Yimeng Yin
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
The protein contains a AT-hook domain.
| null |
b
|
No
|
No
|
No
|
No
| null |
ENSG00000135365
|
PHF21A
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
|
Has a putative AT-hook
| null | null |
SMART has a single AT hook; PMID 11207365 shows it binds DNA non-specifically, supposedly through an HMG box
| null | null | null |
Disagree
|
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null |
AT-hook; check
|
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
|
It is noted above that it has high confidence PWM.
|
will be considered later.
|
x
|
No
|
No
|
Indeterminate - There is no evidence for or against this genes role as a TF___PMIDS:0
|
No
| null |
ENSG00000126464
|
PRR12
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null |
Disagree
|
Disagree
|
Tim Hughes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
It does have two AT hooks on SMART
| null |
Laura Campitelli
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
| null | null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000146285
|
SCML4
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null | null | null |
Matt Weirauch
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
Laura Campitelli
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
Putative polycomb protein by similarity (UniProt Q8N228)
| null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000152217
|
SETBP1
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null |
Orthologous protein from mouse (Setbp1) bind DNA sequence-specifically by PBM
| null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Orthologous protein from mouse (Setbp1) bind DNA sequence-specifically by PBM
| null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
|
AT hook containing protein UniProtKB - Q9Y6X0
|
needs revisit
|
c
|
No
|
No
|
No
|
No
| null |
ENSG00000080603
|
SRCAP
|
AT hook
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null | null | null | null | null | null | null |
Disagree
|
Arttu Jolma
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
Helicase protein that loads H2A.Z into nucleosomes
| null |
Matt Weirauch
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
x
|
No
|
No
|
No
|
No
| null |
ENSG00000188070
|
C11orf95
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null |
Disagree
| null |
Jussi Taipale
|
Likely to be sequence specific TF
|
4 Not a DNA binding protein
| null |
BED domain only; check domain calls and residues required for DNA binding
|
Sam Lambert
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
x
|
Yes
|
No
|
No
|
No
| null |
ENSG00000237765
|
FAM200B
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null | null | null |
Laura Campitelli
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
No
|
No
|
Yes
| null |
ENSG00000141258
|
SGSM2
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null | null | null |
Matt Weirauch
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
Need to decide what to do with BED zinc fingers - there are about 12 of them; and only ZBED1 has a motif (from SELEX).
|
Yes - BED ZFs need to be discussed I think
|
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
No
|
No
|
No
| null |
ENSG00000214717
|
ZBED1
|
BED ZF
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null |
Based on BED ZF Alignment
| null | null | null |
"Has known motif","1 Monomer or homomultimer" has many independent HT-SELEX models from Jolma 2013 and Yin 2017
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000177494
|
ZBED2
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null |
Has a BED domain that should bind DNA, but lacks the dimerization domain (PMID: 20016685).
|
Based on BED ZF Alignment
| null | null | null | null | null |
Disagree
|
Jussi Taipale
|
Unlikely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
BED domain only; check domain calls and residues required for DNA binding
|
Pratyush Das
|
Unlikely to be sequence specific TF
|
3 Low specificity DNA-binding protein
|
PMID: 20016685 says it has BED domain which should bind DNA but lacks the dimerization domain
|
May need a revisit
|
c
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000132846
|
ZBED3
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null | null | null |
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
BED Zf; need to check amino-acids required for DNA binding
|
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000100426
|
ZBED4
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null |
Disagree
| null |
Jussi Taipale
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null |
BED Zf; need to check amino-acids required for DNA binding
|
Laura Campitelli
|
Unlikely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
b
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000236287
|
ZBED5
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null | null | null |
Laura Campitelli
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000257315
|
ZBED6
|
BED ZF
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
| null | null |
Based on BED ZF Alignment
| null |
PMID: 20016685
| null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
ChIP-seq motif in Transfac is probably from this study PMID: 20016685
| null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000221886
|
ZBED8
|
BED ZF
|
No
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
No motif
| null |
Despite its name, does not have a detectable BED ZF domain.
| null |
Despite its name, does not have a detectable BED ZF domain
| null | null | null | null | null |
Jussi Taipale
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null |
BED domain in name but domain not called; check domain calls and residues required for DNA binding
|
Pratyush Das
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
| null | null |
No
|
No
|
No
|
No
|
Yes
| null |
ENSG00000232040
|
ZBED9
|
BED ZF
|
Yes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
No motif
| null | null |
Based on BED ZF Alignment
| null | null | null | null | null | null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
C2H2 SCAN domain
|
needs revisit
|
No
| |||||
ENSG00000106546
|
AHR
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
| null | null | null | null | null | null | null | null |
Tim Hughes
|
Has known motif
|
1 Monomer or homomultimer
|
PMIDS:7592839 claims it binds E-box as a homodimer in vitro; so I put homodimer above.
| null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
|
Can also bind as a heterodimer with ARNT [PMID:12213385]
| null |
other
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:7592839
|
Yes
| null |
ENSG00000063438
|
AHRR
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
| null | null | null | null | null | null |
"1 Monomer or homomultimer" HNGC symbol is AHRR and it is very similar to AHR and should be called accordingly. Based on PMIDS:7592839 AHR can bind as a homodimer. Probably protein however strongly prefers forming heterodimers
| null |
Disagree
|
Tim Hughes
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
Motifs for several orthologs on CisBP. Associated with DNA by ChIP (PMID:17890447)
| null |
Arttu Jolma
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
Based on PMID:17949687 it binds DNA as a heterodimer with ARNT; HNGC-symbol is AHRR
|
HNGC-symbol is AHRR
|
b
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000143437
|
ARNT
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
| null | null | null | null | null | null |
Based on PMID: 7892203 it can bind also as a homodimer. The crystal structure has HIF1A - ARNT heterodimer
| null |
Disagree
|
Jussi Taipale
|
Has known motif
|
2 Obligate heteromer
| null |
most likely obligate heterodimer
|
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:7592839
|
Yes
|
4ZPR
|
ENSG00000172379
|
ARNT2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Matt Weirauch
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:8657146
|
Yes
| null |
ENSG00000133794
|
ARNTL
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; TF PPI_PMIDS:9576906;9616112
|
Yes
|
4H10
|
ENSG00000029153
|
ARNTL2
|
bHLH
|
Yes
|
Inferred motif
|
2 Obligate heteromer
|
High-throughput in vitro
| null |
ARNTL2 Forms heterodimers with CLOCK and NPAS2 (PMID:10864977 ).
| null | null | null | null | null | null | null |
Jussi Taipale
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null |
clone wrong or obligate heterodimer; check also residues
|
Arttu Jolma
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
PMID:10864977 ARNTL2 Forms heterodimers with CLOCK and NPAS2
| null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000139352
|
ASCL1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding; DNA-Binding: sequence-specific_DNA Binding; TF PPI; Transactivation_PMIDS:8662987;8900141
|
Yes
| null |
ENSG00000183734
|
ASCL2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000176009
|
ASCL3
|
bHLH
|
Yes
|
Inferred motif
|
2 Obligate heteromer
|
High-throughput in vitro
| null |
ASCL1 heterodimerizes with TCF3; TCF4 and TCF12 (PMID: 24835951).
| null | null | null | null | null | null | null |
Arttu Jolma
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
ASCL1 heterodimerizes with TCF3; TCF4 and TCF12 PMID: 24835951
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null | null |
a
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000187855
|
ASCL4
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Probably heterodimerizes with TCF3; TCF4 or TCF12 like the other ASCL TFs
| null | null | null | null | null |
Disagree
|
Disagree
|
Arttu Jolma
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
Probably heterodimerizes with TCF3; TCF4 or TCF12 like the other ASCL TFs
| null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Indirect motif has 50% DBD Identity with human/mouse ASCL1. Weak in vitro motifs could be because it prefers to bind as heterodimer with bHLH TCF proteins
|
Missing motif logos/info
|
a
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000232237
|
ASCL5
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Probably heterodimerizes with TCF3; TCF4 or TCF12 like the other ASCL TFs
| null | null | null | null | null | null |
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null |
could need processing or be an obligate heteromer; check amino-acids required for DNA binding
|
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000172238
|
ATOH1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Matt Weirauch
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_Co-activation_PMIDS:14757642
|
Yes
| null |
ENSG00000179774
|
ATOH7
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene Candidate__Transactivation_PMIDS:7721778;15882586;17653051
|
No
| null |
ENSG00000168874
|
ATOH8
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null |
Not clear what is the source of the known motif.
| null |
"Likely to be a sequence specific TF" No, we do not have unpublished data for this. Based on aminoacid sequence the protein seems like a proper bHLH similar to TCF3, TCF4 and TCF12
| null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null |
check amino-acids required for binding
|
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
TF Gene Candidate_DNA-Binding: sequence-specific_Other_PMIDS:11733035;12419857
|
Yes
| null |
ENSG00000180535
|
BHLHA15
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000205899
|
BHLHA9
|
bHLH
|
Yes
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
No motif
| null |
Protein heterodimerizes with TCF3; TCF4 and TCF12 (PMID: 25466284).
| null | null | null | null | null | null | null |
Arttu Jolma
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
Protein heterodimerizes with TCF3; TCF4 and TCF12 and mutations in its DBD causes syndactyly PMID: 25466284
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null | null |
c
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000180828
|
BHLHE22
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000125533
|
BHLHE23
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000134107
|
BHLHE40
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding; DNA-Binding: sequence-specific_DNA Binding_PMIDS:12297495;12397359
|
Yes
| null |
ENSG00000123095
|
BHLHE41
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Tim Hughes
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
b
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific; Transcription Factor Binding: tf co-factor binding_DNA Binding; Other_PMIDS:12657651;15448136
|
Yes
| null |
ENSG00000250709
|
CCDC169-SOHLH2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
| null | null | null | null | null | null |
Protein is a readthrough of SOHLH2 and another gene and has thus identical DBD to SOHLH2 and should thus bind just like it (if it really exists).
|
Disagree
| null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
No
|
Yes
|
No
|
No
|
No
| null |
ENSG00000134852
|
CLOCK
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Can also bind as heterodimer with ARNTL.
| null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
|
Can also bind as heterodimer with ARNTL (see Arttu's comment)
| null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:9616112;15147242;15500444
|
Yes
|
4H10
|
ENSG00000116016
|
EPAS1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
| null | null | null |
(Motif unclear - Matt changed to likely)
| null | null | null | null |
Tim Hughes
|
Has known motif
|
1 Monomer or homomultimer
|
I can't tell where the motifs come from. "HOMER" is not an experimental method - we need to change these entries so it is possible to trace the origin of the data.
|
I can't tell where the motifs come from. "HOMER" is not an experimental method - we need to change these entries so it is possible to trace the origin of the data.
|
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding; DNA-Binding: sequence-specific_Co-activation; DNA Binding_PMIDS:15190133
|
Yes
|
4ZPK
|
ENSG00000146618
|
FERD3L
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000183733
|
FIGLA
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:9362457;15044608
|
No
| null |
ENSG00000113196
|
HAND1
|
bHLH
|
Yes
|
Known motif
|
2 Obligate heteromer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
|
Obligate heteromer (PMID: 10611232).
| null | null |
Literature indicates obligate heterodimer
| null | null | null | null |
Jussi Taipale
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null |
check amino-acids required for binding; could be heteromer
|
Pratyush Das
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
PMID: 10611232
| null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:7791788;11802795;16043483;7671815;15509787;16043483;10611232;16043483
|
Yes
| null |
ENSG00000164107
|
HAND2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_Transcription Factor Binding: tf co-factor binding; DNA-Binding: sequence-specific_TF PPI; Transactivation_PMIDS:11812799;12392994
|
Yes
| null |
ENSG00000187821
|
HELT
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Can form homodimers or heterodimers with HEY2 and HES5, suggesting also that the HELT homodimer is dependent of a additional Orange domain while the HEY2 heterodimer requires just the DBD (PMID: 14764602).
| null | null | null | null | null | null | null |
Arttu Jolma
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
|
PMID: 14764602 shows that it can form homodimers or heterodimers with HEY2 and HES5; suggesting also that the HELT homodimer is dependent of a additional Orange domain while the HEY2 heterodimer requires just the DBD
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:14764602;15071116
|
Yes
| null |
ENSG00000114315
|
HES1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Matt Weirauch
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000069812
|
HES2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Likely also binds as a heterodimer with other bHLH factors
| null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:8354270
|
No
| null |
ENSG00000173673
|
HES3
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null |
"Likely to be a sequence specific TF" - Disagreement is due to inferred motif being classified as "Has known motif", Protein is
|
Disagree
| null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Inferred motif from HES1 (50% DBD Identity)
|
Missing motif logos/info
|
Laura Campitelli
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:10858455
|
No
| null |
ENSG00000188290
|
HES4
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null |
"Likely to be a sequence specific TF" - Disagreement is due to inferred motif being classified as "Has known motif", Protein is
|
Disagree
| null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
Indirect motif has 88% DBD Identity
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
b
|
Yes
|
Yes
|
No
|
No
| null |
ENSG00000197921
|
HES5
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
b
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_TF PPI_PMIDS:15156153
|
Yes
| null |
ENSG00000144485
|
HES6
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
x
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Factor Binding: tf co-factor binding_TF PPI_PMIDS:10851137;10976052
|
Yes
| null |
ENSG00000179111
|
HES7
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Also forms heterodimers.
| null | null | null | null | null | null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
|
also forms heterodimers
| null |
a
|
Yes
|
Yes
|
TF Gene Candidate__Other_PMIDS:11260262;12783854
|
No
| null |
ENSG00000164683
|
HEY1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Factor Binding: tf co-factor binding_Transactivation_PMIDS:16199874
|
Yes
| null |
ENSG00000135547
|
HEY2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Tim Hughes
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000163909
|
HEYL
|
bHLH
|
Yes
|
Inferred motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null |
"Likely to be a sequence specific TF" Protein sequence is almost identical to HEY1 and HEY2 and should bind as homodimer like them
| null |
Disagree
|
Jussi Taipale
|
Likely to be sequence specific TF
|
2 Obligate heteromer
| null |
may be an obligate heterodimer; check for domains and residues required for DNA binding
|
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000100644
|
HIF1A
|
bHLH
|
Yes
|
Known motif
|
2 Obligate heteromer
|
In vivo/Misc source
|
Only known motifs are from Transfac or HocoMoco - origin is uncertain
|
Binds as obligate heteromer with ARNT (PMID: 9027737).
| null | null |
Binds only with ARNT
| null | null | null | null |
Matt Weirauch
|
Has known motif
|
2 Obligate heteromer
|
obligate heteomer evidence: 9027737
|
Yes - somewhat interesting case. Has a (weak) HLH domain. But; I cant find any great evidence that it can bind DNA on its own. Sounds like it can only do so with ARNT.
|
Yimeng Yin
|
Has known motif
|
2 Obligate heteromer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_Transactivation_PMIDS:12133832;15111179;15906272
|
Yes
|
4ZPR
|
ENSG00000124440
|
HIF3A
|
bHLH
|
Yes
|
Inferred motif
|
2 Obligate heteromer
|
In vivo/Misc source
| null |
Binds DNA as a heterodimer with ARNT and ARNT2; reviewed in (PMID: 24099156).
| null | null |
Obligate heterodimer
| null | null | null | null |
Arttu Jolma
|
Has known motif
|
2 Obligate heteromer
|
Binds DNA as a heterodimer with ARNT and ARNT2; reviewed in PMID: 24099156
|
bHLH domain is present in at least the transcript ENST00000300862.7 but it is missing from the annotations. Transfac model is not a bHLH target site
|
Pratyush Das
|
Has known motif
|
2 Obligate heteromer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000125968
|
ID1
|
bHLH
|
No
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
No motif
| null |
ID bHLH proteins lack the basic region and should not be able to bind DNA. The HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
| null | null | null | null |
"5 - not a DNA binding protein" ID bHLH proteins miss the basic region and should not be able to bind DNA, the HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
|
Disagree
| null |
Laura Campitelli
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Yimeng Yin
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Factor Binding: tf co-factor binding_Other_PMIDS:2156629;11234019
|
Yes
| null |
ENSG00000115738
|
ID2
|
bHLH
|
No
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
No motif
| null |
ID bHLH proteins lack the basic region and should not be able to bind DNA. The HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
| null | null | null | null |
"5 - not a DNA binding protein" ID bHLH proteins miss the basic region and should not be able to bind DNA, the HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
| null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
|
bHLH domain is missing the basic region (up to position 14 of the Pfam model).
| null |
Yimeng Yin
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene Candidate__DNA Binding_PMIDS:1922066;7565756
|
Yes
| null |
ENSG00000117318
|
ID3
|
bHLH
|
No
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
No motif
| null |
ID bHLH proteins lack the basic region and should not be able to bind DNA. The HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
| null | null | null | null |
"5 - not a DNA binding protein" ID bHLH proteins miss the basic region and should not be able to bind DNA, the HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
|
Disagree
| null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
Protein is supposed to lack the basic region that bHLH proteins use to bind DNA; however it binds DNA based on PBM
|
Protein is supposed to lack the basic region that bHLH proteins use to bind DNA; however it binds DNA based on PBM
|
Pratyush Das
|
Likely to be sequence specific TF
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene Candidate_Transcription Factor Binding: tf co-factor binding_Other_PMIDS:15016815
|
Yes
| null |
ENSG00000172201
|
ID4
|
bHLH
|
No
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
No motif
| null |
ID bHLH proteins lack the basic region and should not be able to bind DNA. The HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
| null | null | null | null |
"5 - not a DNA binding protein" ID bHLH proteins miss the basic region and should not be able to bind DNA, the HT-SELEX motif for ID4 is likely by a co-precipitated protein or it is a contamination
|
Disagree
|
Disagree
|
Sam Lambert
|
Has known motif
|
2 Obligate heteromer
|
ID bHLH proteins are not canonically thought to have DNA-binding activity. It is possible IFD4 motif the result of being expressed in human cells and pulling-down other bHLH TFs (A. Jolma; personal communication).
| null |
Pratyush Das
|
Unlikely to be sequence specific TF
|
4 Not a DNA binding protein
|
It lacks DNA binding ability but has motif from SELEX
|
needs a revisit
|
c
|
Yes
|
Yes
|
TF Gene Candidate__Transactivation_PMIDS:7665172;8139914
|
No
| null |
ENSG00000104903
|
LYL1
|
bHLH
|
Yes
|
Inferred motif
|
2 Obligate heteromer
|
In vivo/Misc source
| null |
TAL1, TAL2 and LYL are very similar and have a basic region with a bulky tryptophan inserting into the cluster of the basic residues. Binds DNA as a heterodimer with TCF3 (PDB:2YPB and PDB:2YPA).
| null | null | null | null |
"Likely to be sequence specific TF" "2 Obligate heteromer" TAL1, TAL2 and LYL are very similar and have a basic region with a bulky tryptophan inserting into the cluster of the basic residues, yet at least TAL1 binds DNA well as a heterodimer with TCF3. The motifs seem like in vivo motifs except possibly for a one transfac motif. Is known to bind DNA as heterodimer with TCF3 PDB:2YPB and PDB:2YPA
| null | null |
Matt Weirauch
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
Evidence seems to suggest it is an obligate heteromer. Tests on both PBMs and HT-SELEX yielded no motif.
| null |
Pratyush Das
|
Likely to be sequence specific TF
|
2 Obligate heteromer
|
PMID: 22772404
| null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000125952
|
MAX
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:8265351
|
Yes
|
1AN2
|
ENSG00000166823
|
MESP1
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
c
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000188095
|
MESP2
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null |
Seems straightforward
| null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null |
Missing motif logos/info
|
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific; Transcription Factor Binding: tf co-factor binding_Co-activation_PMIDS:16728472
|
No
| null |
ENSG00000187098
|
MITF
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
100%ID - in vitro
| null |
Binds DNA both as homo- and heterodimers (PMID: 23207919). The structure 4ATI is a homodimer with DNA GTTAGCACATGACCCT.
| null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
Based on pmid:23207919; it binds DNA both as homo- and heterodimers; The structure 4ATI is homodimer with DNA GTTAGCACATGACCCT
| null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; Transactivation_PMIDS:14737107;15716956
|
Yes
|
4ATI
|
ENSG00000108788
|
MLX
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Jussi Taipale
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding_PMIDS:10918583;14742444
|
Yes
| null |
ENSG00000175727
|
MLXIP
|
bHLH
|
Yes
|
Inferred motif
|
2 Obligate heteromer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
2 Obligate heteromer
| null | null |
Pratyush Das
|
Has known motif
|
2 Obligate heteromer
| null | null |
a
|
Yes
|
Yes
|
No
|
Yes
| null |
ENSG00000009950
|
MLXIPL
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null | null | null | null | null | null | null | null | null |
Sam Lambert
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific__PMIDS:0
|
Yes
| null |
ENSG00000070444
|
MNT
|
bHLH
|
Yes
|
Known motif
|
1 Monomer or homomultimer
|
High-throughput in vitro
| null |
Prefers to heterodimerize with MAX over homodimer formation (PMID: 9000049).
| null | null | null | null | null | null | null |
Arttu Jolma
|
Has known motif
|
1 Monomer or homomultimer
|
Prefers to heterodimerize with MAX over homodimer formation based on PMID: 9000049
| null |
Pratyush Das
|
Has known motif
|
1 Monomer or homomultimer
| null | null |
a
|
Yes
|
Yes
|
TF Gene_DNA-Binding: sequence-specific_DNA Binding; TF PPI_PMIDS:9184233
|
Yes
| null |
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