SMAD3.H12RSNP.2.P.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SMAD3.H12RSNP.2.P.D
Gene (human)	SMAD3 (GeneCards)
Gene synonyms (human)	MADH3
Gene (mouse)	Smad3
Gene synonyms (mouse)	Madh3
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	14
Consensus	vWRSWGnSAGMSWv
GC content	55.94%
Information content (bits; total / per base)	9.914 / 0.708
Data sources	ChIP-Seq
Aligned words	1027

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	4 (24)	0.614	0.742	0.417	0.6	0.629	0.744	1.509	2.357	8.488	55.509
Mouse	1 (5)	0.582	0.585	0.404	0.411	0.602	0.613	1.465	1.488	1.886	3.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.621	0.583	0.578	0.557	0.547	0.538
Non-Methyl HT-SELEX, 2 experiments	best	0.64	0.598	0.589	0.566	0.555	0.545

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	R-MAD {7.1.1.1} (TFClass)
TFClass ID	TFClass: 7.1.1.1.3
HGNC	HGNC:6769
MGI	MGI:1201674
EntrezGene (human)	GeneID:4088 (SSTAR profile)
EntrezGene (mouse)	GeneID:17127 (SSTAR profile)
UniProt ID (human)	SMAD3_HUMAN
UniProt ID (mouse)	SMAD3_MOUSE
UniProt AC (human)	P84022 (TFClass)
UniProt AC (mouse)	Q8BUN5 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	4 human, 1 mouse
HT-SELEX	2
Methyl-HT-SELEX	0

PCM	SMAD3.H12RSNP.2.P.D.pcm
PWM	SMAD3.H12RSNP.2.P.D.pwm
PFM	SMAD3.H12RSNP.2.P.D.pfm
Alignment	SMAD3.H12RSNP.2.P.D.words.tsv
Threshold to P-value map	SMAD3.H12RSNP.2.P.D.thr
Motif in other formats
JASPAR format	SMAD3.H12RSNP.2.P.D_jaspar_format.txt
MEME format	SMAD3.H12RSNP.2.P.D_meme_format.meme
Transfac format	SMAD3.H12RSNP.2.P.D_transfac_format.txt
Homer format	SMAD3.H12RSNP.2.P.D_homer_format_0.001.txt SMAD3.H12RSNP.2.P.D_homer_format_0.0005.txt SMAD3.H12RSNP.2.P.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	216.0	431.0	228.0	152.0
02	669.0	59.0	146.0	153.0
03	167.0	46.0	700.0	114.0
04	52.0	278.0	661.0	36.0
05	288.0	27.0	66.0	646.0
06	19.0	33.0	955.0	20.0
07	313.0	289.0	242.0	183.0
08	61.0	598.0	254.0	114.0
09	977.0	2.0	12.0	36.0
10	33.0	28.0	948.0	18.0
11	642.0	206.0	129.0	50.0
12	54.0	791.0	104.0	78.0
13	637.0	56.0	83.0	251.0
14	199.0	221.0	450.0	157.0

PFM

	A	C	G	T
01	0.21	0.42	0.222	0.148
02	0.651	0.057	0.142	0.149
03	0.163	0.045	0.682	0.111
04	0.051	0.271	0.644	0.035
05	0.28	0.026	0.064	0.629
06	0.019	0.032	0.93	0.019
07	0.305	0.281	0.236	0.178
08	0.059	0.582	0.247	0.111
09	0.951	0.002	0.012	0.035
10	0.032	0.027	0.923	0.018
11	0.625	0.201	0.126	0.049
12	0.053	0.77	0.101	0.076
13	0.62	0.055	0.081	0.244
14	0.194	0.215	0.438	0.153

PWM

	A	C	G	T
01	-0.172	0.515	-0.118	-0.52
02	0.954	-1.448	-0.559	-0.513
03	-0.427	-1.689	0.999	-0.804
04	-1.571	0.079	0.942	-1.924
05	0.114	-2.197	-1.339	0.919
06	-2.523	-2.007	1.309	-2.476
07	0.197	0.118	-0.059	-0.336
08	-1.416	0.842	-0.011	-0.804
09	1.331	-4.237	-2.935	-1.924
10	-2.007	-2.163	1.301	-2.573
11	0.912	-0.219	-0.682	-1.609
12	-1.534	1.121	-0.894	-1.176
13	0.905	-1.499	-1.115	-0.022
14	-0.253	-0.149	0.558	-0.488

Standard thresholds

P-value	Threshold
0.001	4.72251
0.0005	5.53091
0.0001	7.19446