SMAD3.H12INVITRO.0.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SMAD3.H12INVITRO.0.S.B
Gene (human)	SMAD3 (GeneCards)
Gene synonyms (human)	MADH3
Gene (mouse)	Smad3
Gene synonyms (mouse)	Madh3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	RWCTAGACAbn
GC content	48.18%
Information content (bits; total / per base)	13.89 / 1.263
Data sources	HT-SELEX
Aligned words	6936

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)	0.792	0.835	0.648	0.711	0.735	0.776	2.114	2.345	60.184	75.328
Mouse	1 (5)	0.63	0.641	0.477	0.493	0.599	0.605	1.51	1.552	8.469	15.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 2 experiments	median	0.883	0.852	0.752	0.739	0.637	0.649
Non-Methyl HT-SELEX, 2 experiments	best	0.919	0.897	0.788	0.777	0.657	0.673

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.0.S.B.pcm
PWM	SMAD3.H12INVITRO.0.S.B.pwm
PFM	SMAD3.H12INVITRO.0.S.B.pfm
Alignment	SMAD3.H12INVITRO.0.S.B.words.tsv
Threshold to P-value map	SMAD3.H12INVITRO.0.S.B.thr
Motif in other formats
JASPAR format	SMAD3.H12INVITRO.0.S.B_jaspar_format.txt
MEME format	SMAD3.H12INVITRO.0.S.B_meme_format.meme
Transfac format	SMAD3.H12INVITRO.0.S.B_transfac_format.txt
Homer format	SMAD3.H12INVITRO.0.S.B_homer_format_0.001.txt SMAD3.H12INVITRO.0.S.B_homer_format_0.0005.txt SMAD3.H12INVITRO.0.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	947.5	511.5	4874.5	602.5
02	889.25	551.25	717.25	4778.25
03	33.0	6848.0	28.0	27.0
04	0.0	1125.0	4.0	5807.0
05	6936.0	0.0	0.0	0.0
06	0.0	0.0	6936.0	0.0
07	6936.0	0.0	0.0	0.0
08	0.0	6936.0	0.0	0.0
09	5076.0	7.0	1701.0	152.0
10	638.75	734.75	2244.75	3317.75
11	1309.75	1646.75	1893.75	2085.75

PFM

	A	C	G	T
01	0.137	0.074	0.703	0.087
02	0.128	0.079	0.103	0.689
03	0.005	0.987	0.004	0.004
04	0.0	0.162	0.001	0.837
05	1.0	0.0	0.0	0.0
06	0.0	0.0	1.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	1.0	0.0	0.0
09	0.732	0.001	0.245	0.022
10	0.092	0.106	0.324	0.478
11	0.189	0.237	0.273	0.301

PWM

	A	C	G	T
01	-0.603	-1.218	1.033	-1.055
02	-0.667	-1.143	-0.881	1.013
03	-3.898	1.373	-4.051	-4.085
04	-6.666	-0.432	-5.633	1.208
05	1.385	-6.666	-6.666	-6.666
06	-6.666	-6.666	1.385	-6.666
07	1.385	-6.666	-6.666	-6.666
08	-6.666	1.385	-6.666	-6.666
09	1.073	-5.239	-0.019	-2.421
10	-0.996	-0.857	0.258	0.648
11	-0.28	-0.052	0.088	0.184

Standard thresholds

P-value	Threshold
0.001	1.411325
0.0005	2.998875
0.0001	7.047795