SMAD3.H12INVITRO.2.P.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SMAD3.H12INVITRO.2.P.C
Gene (human)	SMAD3 (GeneCards)
Gene synonyms (human)	MADH3
Gene (mouse)	Smad3
Gene synonyms (mouse)	Madh3
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	C

Motif length	13
Consensus	RRSWGnbAGRCWv
GC content	56.08%
Information content (bits; total / per base)	9.812 / 0.755
Data sources	ChIP-Seq
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	4 (24)	0.611	0.733	0.418	0.588	0.627	0.741	1.524	2.335	7.394	47.721
Mouse	1 (5)	0.567	0.578	0.393	0.399	0.601	0.617	1.465	1.501	2.268	2.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.629	0.594	0.581	0.562	0.549	0.541
Non-Methyl HT-SELEX, 2 experiments	best	0.649	0.61	0.594	0.573	0.557	0.548

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.H12INVITRO.2.P.C.pcm
PWM	SMAD3.H12INVITRO.2.P.C.pwm
PFM	SMAD3.H12INVITRO.2.P.C.pfm
Alignment	SMAD3.H12INVITRO.2.P.C.words.tsv
Threshold to P-value map	SMAD3.H12INVITRO.2.P.C.thr
Motif in other formats
JASPAR format	SMAD3.H12INVITRO.2.P.C_jaspar_format.txt
MEME format	SMAD3.H12INVITRO.2.P.C_meme_format.meme
Transfac format	SMAD3.H12INVITRO.2.P.C_transfac_format.txt
Homer format	SMAD3.H12INVITRO.2.P.C_homer_format_0.001.txt SMAD3.H12INVITRO.2.P.C_homer_format_0.0005.txt SMAD3.H12INVITRO.2.P.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	553.0	36.0	250.0	161.0
02	166.0	27.0	688.0	119.0
03	86.0	212.0	667.0	35.0
04	241.0	33.0	91.0	635.0
05	35.0	25.0	925.0	15.0
06	331.0	242.0	254.0	173.0
07	61.0	552.0	265.0	122.0
08	962.0	0.0	17.0	21.0
09	38.0	27.0	916.0	19.0
10	579.0	160.0	201.0	60.0
11	46.0	812.0	101.0	41.0
12	649.0	50.0	59.0	242.0
13	163.0	183.0	497.0	157.0

PFM

	A	C	G	T
01	0.553	0.036	0.25	0.161
02	0.166	0.027	0.688	0.119
03	0.086	0.212	0.667	0.035
04	0.241	0.033	0.091	0.635
05	0.035	0.025	0.925	0.015
06	0.331	0.242	0.254	0.173
07	0.061	0.552	0.265	0.122
08	0.962	0.0	0.017	0.021
09	0.038	0.027	0.916	0.019
10	0.579	0.16	0.201	0.06
11	0.046	0.812	0.101	0.041
12	0.649	0.05	0.059	0.242
13	0.163	0.183	0.497	0.157

PWM

	A	C	G	T
01	0.79	-1.898	0.0	-0.436
02	-0.406	-2.171	1.008	-0.735
03	-1.054	-0.164	0.977	-1.925
04	-0.036	-1.981	-0.999	0.928
05	-1.925	-2.243	1.303	-2.711
06	0.279	-0.032	0.016	-0.365
07	-1.39	0.788	0.058	-0.71
08	1.342	-4.982	-2.598	-2.405
09	-1.846	-2.171	1.294	-2.497
10	0.836	-0.442	-0.216	-1.406
11	-1.663	1.173	-0.896	-1.774
12	0.95	-1.582	-1.422	-0.032
13	-0.424	-0.309	0.684	-0.461

Standard thresholds

P-value	Threshold
0.001	4.74896
0.0005	5.55556
0.0001	7.207265