HTF4.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HTF4.H12INVITRO.0.PSM.A
Gene (human)	TCF12 (GeneCards)
Gene synonyms (human)	BHLHB20, HEB, HTF4
Gene (mouse)	Tcf12
Gene synonyms (mouse)	Alf1, Meb
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	8
Consensus	vCAGGTGn
GC content	64.77%
Information content (bits; total / per base)	12.142 / 1.518
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	6817

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	8 (55)	0.703	0.791	0.578	0.672	0.748	0.85	2.003	2.537	80.018	202.398
Mouse	4 (28)	0.689	0.739	0.589	0.664	0.702	0.746	1.819	2.036	74.528	115.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.968	0.943	0.957	0.929	0.915	0.887
Overall, 4 experiments	best	0.971	0.949	0.964	0.939	0.93	0.902
Methyl HT-SELEX, 2 experiments	median	0.968	0.944	0.959	0.931	0.915	0.887
Methyl HT-SELEX, 2 experiments	best	0.971	0.949	0.964	0.939	0.927	0.901
Non-Methyl HT-SELEX, 2 experiments	median	0.955	0.924	0.938	0.903	0.886	0.854
Non-Methyl HT-SELEX, 2 experiments	best	0.97	0.947	0.961	0.934	0.93	0.902

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.332	2.381	0.077	0.04

TF superclass	Basic domains {1} (TFClass)
TF class	Basic helix-loop-helix factors (bHLH) {1.2} (TFClass)
TF family	E2A {1.2.1} (TFClass)
TF subfamily	E2A-like {1.2.1.0} (TFClass)
TFClass ID	TFClass: 1.2.1.0.3
HGNC	HGNC:11623
MGI	MGI:101877
EntrezGene (human)	GeneID:6938 (SSTAR profile)
EntrezGene (mouse)	GeneID:21406 (SSTAR profile)
UniProt ID (human)	HTF4_HUMAN
UniProt ID (mouse)	HTF4_MOUSE
UniProt AC (human)	Q99081 (TFClass)
UniProt AC (mouse)	Q61286 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	8 human, 4 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	HTF4.H12INVITRO.0.PSM.A.pcm
PWM	HTF4.H12INVITRO.0.PSM.A.pwm
PFM	HTF4.H12INVITRO.0.PSM.A.pfm
Alignment	HTF4.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	HTF4.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	HTF4.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	HTF4.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	HTF4.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	HTF4.H12INVITRO.0.PSM.A_homer_format_0.001.txt HTF4.H12INVITRO.0.PSM.A_homer_format_0.0005.txt HTF4.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1481.75	1386.75	2818.75	1129.75
02	0.0	6817.0	0.0	0.0
03	6817.0	0.0	0.0	0.0
04	0.0	0.0	6817.0	0.0
05	0.0	0.0	6817.0	0.0
06	0.0	0.0	0.0	6817.0
07	0.0	0.0	6817.0	0.0
08	1100.5	2240.5	1606.5	1869.5

PFM

	A	C	G	T
01	0.217	0.203	0.413	0.166
02	0.0	1.0	0.0	0.0
03	1.0	0.0	0.0	0.0
04	0.0	0.0	1.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	1.0	0.0
08	0.161	0.329	0.236	0.274

PWM

	A	C	G	T
01	-0.14	-0.206	0.503	-0.41
02	-6.651	1.385	-6.651	-6.651
03	1.385	-6.651	-6.651	-6.651
04	-6.651	-6.651	1.385	-6.651
05	-6.651	-6.651	1.385	-6.651
06	-6.651	-6.651	-6.651	1.385
07	-6.651	-6.651	1.385	-6.651
08	-0.437	0.273	-0.059	0.092

Standard thresholds

P-value	Threshold
0.001	0.58818
0.0005	1.29169
0.0001	8.24112