ITF2.H14INVITRO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ITF2.H14INVITRO.1.PSM.A
Gene (human)	TCF4 (GeneCards)
Gene synonyms (human)	BHLHB19, ITF2, SEF2
Gene (mouse)	Tcf4
Gene synonyms (mouse)	Itf2, Sef2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	10
Consensus	nRCAGGTGbn
GC content	62.12%
Information content (bits; total / per base)	12.939 / 1.294
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1424
Previous names	ITF2.H12INVITRO.1.PSM.A

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)	0.739	0.912	0.612	0.779	0.762	0.919	2.103	3.138	92.824	204.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.98	0.965	0.975	0.957	0.95	0.93
Overall, 6 experiments	best	0.997	0.994	0.996	0.993	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.982	0.968	0.978	0.961	0.953	0.934
Methyl HT-SELEX, 1 experiments	best	0.982	0.968	0.978	0.961	0.953	0.934
Non-Methyl HT-SELEX, 5 experiments	median	0.979	0.962	0.973	0.954	0.947	0.926
Non-Methyl HT-SELEX, 5 experiments	best	0.997	0.994	0.996	0.993	0.995	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	3.626	17.508	0.165	0.155

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: 1.2.1.0.2
HGNC	HGNC:11634
MGI	MGI:98506
EntrezGene (human)	GeneID:6925 (SSTAR profile)
EntrezGene (mouse)	GeneID:21413 (SSTAR profile)
UniProt ID (human)	ITF2_HUMAN
UniProt ID (mouse)	ITF2_MOUSE
UniProt AC (human)	P15884 (TFClass)
UniProt AC (mouse)	Q60722 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	8 human, 0 mouse
HT-SELEX	5
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	ITF2.H14INVITRO.1.PSM.A.pcm
PWM	ITF2.H14INVITRO.1.PSM.A.pwm
PFM	ITF2.H14INVITRO.1.PSM.A.pfm
Threshold to P-value map	ITF2.H14INVITRO.1.PSM.A.thr
Motif in other formats
JASPAR format	ITF2.H14INVITRO.1.PSM.A_jaspar_format.txt
MEME format	ITF2.H14INVITRO.1.PSM.A_meme_format.meme
Transfac format	ITF2.H14INVITRO.1.PSM.A_transfac_format.txt
Homer format	ITF2.H14INVITRO.1.PSM.A_homer_format_0.001.txt ITF2.H14INVITRO.1.PSM.A_homer_format_0.0005.txt ITF2.H14INVITRO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	361.0	264.0	326.0	473.0
02	349.0	197.0	845.0	33.0
03	0.0	1424.0	0.0	0.0
04	1424.0	0.0	0.0	0.0
05	0.0	0.0	1424.0	0.0
06	0.0	0.0	1424.0	0.0
07	0.0	0.0	0.0	1424.0
08	0.0	0.0	1424.0	0.0
09	80.0	660.0	212.0	472.0
10	434.75	204.75	440.75	343.75

PFM

	A	C	G	T
01	0.254	0.185	0.229	0.332
02	0.245	0.138	0.593	0.023
03	0.0	1.0	0.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.056	0.463	0.149	0.331
10	0.305	0.144	0.31	0.241

PWM

	A	C	G	T
01	0.014	-0.297	-0.088	0.283
02	-0.02	-0.588	0.861	-2.33
03	-5.284	1.382	-5.284	-5.284
04	1.382	-5.284	-5.284	-5.284
05	-5.284	-5.284	1.382	-5.284
06	-5.284	-5.284	1.382	-5.284
07	-5.284	-5.284	-5.284	1.382
08	-5.284	-5.284	1.382	-5.284
09	-1.476	0.615	-0.515	0.281
10	0.199	-0.549	0.213	-0.035

Standard thresholds

P-value	Threshold
0.001	2.172555
0.0005	2.984285
0.0001	7.950505