HTF4.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HTF4.H12INVIVO.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	11
Consensus	dvdSCAGSTGb
GC content	62.89%
Information content (bits; total / per base)	11.56 / 1.051
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1000

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)	0.847	0.896	0.713	0.783	0.793	0.884	2.244	2.965	105.131	298.745
Mouse	4 (28)	0.791	0.842	0.665	0.741	0.718	0.782	2.074	2.366	101.626	156.523

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.956	0.917	0.954	0.916	0.915	0.881
Overall, 4 experiments	best	0.958	0.922	0.957	0.92	0.93	0.896
Methyl HT-SELEX, 2 experiments	median	0.958	0.922	0.956	0.92	0.922	0.889
Methyl HT-SELEX, 2 experiments	best	0.958	0.922	0.957	0.92	0.93	0.896
Non-Methyl HT-SELEX, 2 experiments	median	0.943	0.899	0.931	0.888	0.873	0.837
Non-Methyl HT-SELEX, 2 experiments	best	0.954	0.913	0.953	0.914	0.915	0.88

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.061	2.096	0.104	0.058

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.H12INVIVO.0.PSM.A.pcm
PWM	HTF4.H12INVIVO.0.PSM.A.pwm
PFM	HTF4.H12INVIVO.0.PSM.A.pfm
Alignment	HTF4.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	HTF4.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	HTF4.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	HTF4.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	HTF4.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	HTF4.H12INVIVO.0.PSM.A_homer_format_0.001.txt HTF4.H12INVIVO.0.PSM.A_homer_format_0.0005.txt HTF4.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	369.0	134.0	351.0	146.0
02	207.0	368.0	330.0	95.0
03	467.0	119.0	246.0	168.0
04	155.0	248.0	588.0	9.0
05	4.0	991.0	4.0	1.0
06	996.0	0.0	1.0	3.0
07	4.0	3.0	990.0	3.0
08	63.0	475.0	456.0	6.0
09	2.0	2.0	10.0	986.0
10	1.0	5.0	989.0	5.0
11	31.0	330.0	278.0	361.0

PFM

	A	C	G	T
01	0.369	0.134	0.351	0.146
02	0.207	0.368	0.33	0.095
03	0.467	0.119	0.246	0.168
04	0.155	0.248	0.588	0.009
05	0.004	0.991	0.004	0.001
06	0.996	0.0	0.001	0.003
07	0.004	0.003	0.99	0.003
08	0.063	0.475	0.456	0.006
09	0.002	0.002	0.01	0.986
10	0.001	0.005	0.989	0.005
11	0.031	0.33	0.278	0.361

PWM

	A	C	G	T
01	0.387	-0.618	0.337	-0.533
02	-0.187	0.384	0.276	-0.956
03	0.622	-0.735	-0.016	-0.394
04	-0.474	-0.008	0.851	-3.156
05	-3.783	1.372	-3.783	-4.525
06	1.377	-4.982	-4.525	-3.975
07	-3.783	-3.975	1.371	-3.975
08	-1.358	0.639	0.598	-3.484
09	-4.213	-4.213	-3.066	1.367
10	-4.525	-3.622	1.37	-3.622
11	-2.04	0.276	0.105	0.365

Standard thresholds

P-value	Threshold
0.001	3.6313
0.0005	4.802215
0.0001	7.859515