ITF2.H12CORE.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ITF2.H12CORE.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	nvCAGGTGYd
GC content	61.27%
Information content (bits; total / per base)	13.203 / 1.32
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)	0.84	0.918	0.604	0.796	0.795	0.94	2.101	3.589	103.509	213.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.978	0.96	0.974	0.953	0.964	0.942
Overall, 6 experiments	best	0.997	0.994	0.996	0.993	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.979	0.963	0.976	0.958	0.97	0.949
Methyl HT-SELEX, 1 experiments	best	0.979	0.963	0.976	0.958	0.97	0.949
Non-Methyl HT-SELEX, 5 experiments	median	0.976	0.956	0.971	0.949	0.959	0.935
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
#	4.056	20.903	0.175	0.164

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

PCM	ITF2.H12CORE.1.PSM.A.pcm
PWM	ITF2.H12CORE.1.PSM.A.pwm
PFM	ITF2.H12CORE.1.PSM.A.pfm
Alignment	ITF2.H12CORE.1.PSM.A.words.tsv
Threshold to P-value map	ITF2.H12CORE.1.PSM.A.thr
Motif in other formats
JASPAR format	ITF2.H12CORE.1.PSM.A_jaspar_format.txt
MEME format	ITF2.H12CORE.1.PSM.A_meme_format.meme
Transfac format	ITF2.H12CORE.1.PSM.A_transfac_format.txt
Homer format	ITF2.H12CORE.1.PSM.A_homer_format_0.001.txt ITF2.H12CORE.1.PSM.A_homer_format_0.0005.txt ITF2.H12CORE.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	202.0	194.0	258.0	346.0
02	299.0	345.0	351.0	5.0
03	1.0	999.0	0.0	0.0
04	1000.0	0.0	0.0	0.0
05	0.0	0.0	1000.0	0.0
06	3.0	25.0	972.0	0.0
07	0.0	0.0	0.0	1000.0
08	0.0	0.0	1000.0	0.0
09	16.0	188.0	151.0	645.0
10	140.0	83.0	561.0	216.0

PFM

	A	C	G	T
01	0.202	0.194	0.258	0.346
02	0.299	0.345	0.351	0.005
03	0.001	0.999	0.0	0.0
04	1.0	0.0	0.0	0.0
05	0.0	0.0	1.0	0.0
06	0.003	0.025	0.972	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.016	0.188	0.151	0.645
10	0.14	0.083	0.561	0.216

PWM

	A	C	G	T
01	-0.212	-0.252	0.031	0.323
02	0.178	0.32	0.337	-3.622
03	-4.525	1.38	-4.982	-4.982
04	1.381	-4.982	-4.982	-4.982
05	-4.982	-4.982	1.381	-4.982
06	-3.975	-2.243	1.353	-4.982
07	-4.982	-4.982	-4.982	1.381
08	-4.982	-4.982	1.381	-4.982
09	-2.653	-0.283	-0.5	0.944
10	-0.574	-1.089	0.804	-0.145

Standard thresholds

P-value	Threshold
0.001	2.64681
0.0005	3.72352
0.0001	7.55124