ITF2.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	ITF2.H12RSNP.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	nSCAGGTGYd
GC content	61.84%
Information content (bits; total / per base)	13.318 / 1.332
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1001

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)	0.848	0.921	0.616	0.802	0.8	0.94	2.13	3.576	108.959	231.292

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 6 experiments	median	0.977	0.957	0.973	0.952	0.962	0.939
Overall, 6 experiments	best	0.997	0.994	0.997	0.993	0.995	0.992
Methyl HT-SELEX, 1 experiments	median	0.979	0.96	0.976	0.956	0.967	0.946
Methyl HT-SELEX, 1 experiments	best	0.979	0.96	0.976	0.956	0.967	0.946
Non-Methyl HT-SELEX, 5 experiments	median	0.975	0.955	0.97	0.948	0.956	0.931
Non-Methyl HT-SELEX, 5 experiments	best	0.997	0.994	0.997	0.993	0.995	0.992

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	4.092	20.928	0.176	0.162

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.H12RSNP.1.PSM.A.pcm
PWM	ITF2.H12RSNP.1.PSM.A.pwm
PFM	ITF2.H12RSNP.1.PSM.A.pfm
Alignment	ITF2.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	ITF2.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	ITF2.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	ITF2.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	ITF2.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	ITF2.H12RSNP.1.PSM.A_homer_format_0.001.txt ITF2.H12RSNP.1.PSM.A_homer_format_0.0005.txt ITF2.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	190.0	158.0	310.0	343.0
02	247.0	452.0	302.0	0.0
03	0.0	1001.0	0.0	0.0
04	1001.0	0.0	0.0	0.0
05	0.0	0.0	1001.0	0.0
06	2.0	39.0	960.0	0.0
07	0.0	0.0	0.0	1001.0
08	0.0	0.0	1001.0	0.0
09	6.0	208.0	113.0	674.0
10	122.0	114.0	531.0	234.0

PFM

	A	C	G	T
01	0.19	0.158	0.31	0.343
02	0.247	0.452	0.302	0.0
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	0.002	0.039	0.959	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.006	0.208	0.113	0.673
10	0.122	0.114	0.53	0.234

PWM

	A	C	G	T
01	-0.273	-0.456	0.213	0.313
02	-0.013	0.588	0.187	-4.983
03	-4.983	1.381	-4.983	-4.983
04	1.381	-4.983	-4.983	-4.983
05	-4.983	-4.983	1.381	-4.983
06	-4.214	-1.822	1.339	-4.983
07	-4.983	-4.983	-4.983	1.381
08	-4.983	-4.983	1.381	-4.983
09	-3.485	-0.184	-0.787	0.986
10	-0.711	-0.778	0.749	-0.067

Standard thresholds

P-value	Threshold
0.001	2.568635
0.0005	3.594805
0.0001	7.583835