SMAD4.H12INVIVO.1.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SMAD4.H12INVIVO.1.P.B
Gene (human)	SMAD4 (GeneCards)
Gene synonyms (human)	DPC4, MADH4
Gene (mouse)	Smad4
Gene synonyms (mouse)	Dpc4, Madh4
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	vWGKCTSdCWSYh
GC content	55.97%
Information content (bits; total / per base)	11.066 / 0.851
Data sources	ChIP-Seq
Aligned words	1021

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	5 (29)	0.624	0.874	0.446	0.8	0.606	0.878	1.562	3.854	13.886	222.745
Mouse	1 (5)	0.688	0.701	0.58	0.6	0.67	0.705	2.464	2.595	44.215	71.155

TF superclass	beta-Hairpin exposed by an alpha/beta-scaffold {7} (TFClass)
TF class	SMAD/NF-1 DNA-binding domain factors {7.1} (TFClass)
TF family	SMAD {7.1.1} (TFClass)
TF subfamily	Co-SMAD {7.1.1.2} (TFClass)
TFClass ID	TFClass: 7.1.1.2.1
HGNC	HGNC:6770
MGI	MGI:894293
EntrezGene (human)	GeneID:4089 (SSTAR profile)
EntrezGene (mouse)	GeneID:17128 (SSTAR profile)
UniProt ID (human)	SMAD4_HUMAN
UniProt ID (mouse)	SMAD4_MOUSE
UniProt AC (human)	Q13485 (TFClass)
UniProt AC (mouse)	P97471 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	5 human, 1 mouse
HT-SELEX	0
Methyl-HT-SELEX	0

PCM	SMAD4.H12INVIVO.1.P.B.pcm
PWM	SMAD4.H12INVIVO.1.P.B.pwm
PFM	SMAD4.H12INVIVO.1.P.B.pfm
Alignment	SMAD4.H12INVIVO.1.P.B.words.tsv
Threshold to P-value map	SMAD4.H12INVIVO.1.P.B.thr
Motif in other formats
JASPAR format	SMAD4.H12INVIVO.1.P.B_jaspar_format.txt
MEME format	SMAD4.H12INVIVO.1.P.B_meme_format.meme
Transfac format	SMAD4.H12INVIVO.1.P.B_transfac_format.txt
Homer format	SMAD4.H12INVIVO.1.P.B_homer_format_0.001.txt SMAD4.H12INVIVO.1.P.B_homer_format_0.0005.txt SMAD4.H12INVIVO.1.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	207.0	438.0	226.0	150.0
02	256.0	125.0	48.0	592.0
03	22.0	20.0	968.0	11.0
04	43.0	52.0	146.0	780.0
05	4.0	997.0	11.0	9.0
06	6.0	6.0	2.0	1007.0
07	141.0	210.0	632.0	38.0
08	221.0	134.0	381.0	285.0
09	34.0	907.0	52.0	28.0
10	743.0	36.0	95.0	147.0
11	69.0	762.0	150.0	40.0
12	134.0	607.0	71.0	209.0
13	136.0	251.0	102.0	532.0

PFM

	A	C	G	T
01	0.203	0.429	0.221	0.147
02	0.251	0.122	0.047	0.58
03	0.022	0.02	0.948	0.011
04	0.042	0.051	0.143	0.764
05	0.004	0.976	0.011	0.009
06	0.006	0.006	0.002	0.986
07	0.138	0.206	0.619	0.037
08	0.216	0.131	0.373	0.279
09	0.033	0.888	0.051	0.027
10	0.728	0.035	0.093	0.144
11	0.068	0.746	0.147	0.039
12	0.131	0.595	0.07	0.205
13	0.133	0.246	0.1	0.521

PWM

	A	C	G	T
01	-0.208	0.537	-0.121	-0.527
02	0.003	-0.707	-1.642	0.837
03	-2.382	-2.47	1.328	-3.005
04	-1.748	-1.565	-0.554	1.113
05	-3.803	1.357	-3.005	-3.176
06	-3.504	-3.504	-4.232	1.367
07	-0.588	-0.194	0.903	-1.867
08	-0.143	-0.638	0.398	0.11
09	-1.973	1.263	-1.565	-2.157
10	1.064	-1.918	-0.977	-0.547
11	-1.29	1.089	-0.527	-1.818
12	-0.638	0.862	-1.262	-0.198
13	-0.624	-0.017	-0.907	0.731

Standard thresholds

P-value	Threshold
0.001	4.48091
0.0005	5.39206
0.0001	7.24893