SOX3.H13RSNP.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H13RSNP.1.S.C
Gene (human)	SOX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox3
Gene synonyms (mouse)	Sox-3
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	16
Consensus	hWWKdbMATTGTbvbn
GC content	39.63%
Information content (bits; total / per base)	13.843 / 0.865
Data sources	HT-SELEX
Aligned words	1487
Previous names	SOX3.H12RSNP.1.S.C

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	1 (7)	0.623	0.646	0.446	0.502	0.646	0.692	1.579	1.754	13.06	24.721
Mouse	3 (11)	0.671	0.688	0.506	0.523	0.618	0.656	1.529	1.663	34.678	52.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.987	0.982	0.972	0.96	0.938	0.92
Overall, 2 experiments	best	0.998	0.997	0.991	0.988	0.965	0.957
Methyl HT-SELEX, 1 experiments	median	0.976	0.966	0.952	0.932	0.91	0.883
Methyl HT-SELEX, 1 experiments	best	0.976	0.966	0.952	0.932	0.91	0.883
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.991	0.988	0.965	0.957
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.991	0.988	0.965	0.957

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.665	0.361	0.597	0.475

TF superclass	Other all-alpha-helical DNA-binding domains {4} (TFClass)
TF class	High-mobility group (HMG) domain factors {4.1} (TFClass)
TF family	SOX-related {4.1.1} (TFClass)
TF subfamily	Group B {4.1.1.2} (TFClass)
TFClass ID	TFClass: 4.1.1.2.3
HGNC	HGNC:11199
MGI	MGI:98365
EntrezGene (human)	GeneID:6658 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	SOX3_HUMAN
UniProt ID (mouse)	SOX3_MOUSE
UniProt AC (human)	P41225 (TFClass)
UniProt AC (mouse)	P53784 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 3 mouse
HT-SELEX	1
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SOX3.H13RSNP.1.S.C.pcm
PWM	SOX3.H13RSNP.1.S.C.pwm
PFM	SOX3.H13RSNP.1.S.C.pfm
Threshold to P-value map	SOX3.H13RSNP.1.S.C.thr
Motif in other formats
JASPAR format	SOX3.H13RSNP.1.S.C_jaspar_format.txt
MEME format	SOX3.H13RSNP.1.S.C_meme_format.meme
Transfac format	SOX3.H13RSNP.1.S.C_transfac_format.txt
Homer format	SOX3.H13RSNP.1.S.C_homer_format_0.001.txt SOX3.H13RSNP.1.S.C_homer_format_0.0005.txt SOX3.H13RSNP.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	411.0	817.0	111.0	148.0
02	1154.0	90.0	104.0	139.0
03	971.0	36.0	72.0	408.0
04	108.0	64.0	210.0	1105.0
05	312.0	95.0	801.0	279.0
06	143.0	757.0	324.0	263.0
07	265.0	1062.0	1.0	159.0
08	1487.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1487.0
10	0.0	0.0	0.0	1487.0
11	0.0	0.0	1487.0	0.0
12	297.0	38.0	3.0	1149.0
13	125.0	509.0	246.0	607.0
14	386.0	585.0	312.0	204.0
15	194.5	587.5	292.5	412.5
16	261.75	431.75	393.75	399.75

PFM

	A	C	G	T
01	0.276	0.549	0.075	0.1
02	0.776	0.061	0.07	0.093
03	0.653	0.024	0.048	0.274
04	0.073	0.043	0.141	0.743
05	0.21	0.064	0.539	0.188
06	0.096	0.509	0.218	0.177
07	0.178	0.714	0.001	0.107
08	1.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.0	0.0	1.0
11	0.0	0.0	1.0	0.0
12	0.2	0.026	0.002	0.773
13	0.084	0.342	0.165	0.408
14	0.26	0.393	0.21	0.137
15	0.131	0.395	0.197	0.277
16	0.176	0.29	0.265	0.269

PWM

	A	C	G	T
01	0.1	0.785	-1.197	-0.914
02	1.129	-1.403	-1.261	-0.976
03	0.957	-2.29	-1.621	0.093
04	-1.224	-1.736	-0.567	1.086
05	-0.174	-1.35	0.765	-0.285
06	-0.948	0.709	-0.137	-0.344
07	-0.337	1.047	-4.884	-0.843
08	1.383	-5.321	-5.321	-5.321
09	-5.321	-5.321	-5.321	1.383
10	-5.321	-5.321	-5.321	1.383
11	-5.321	-5.321	1.383	-5.321
12	-0.223	-2.239	-4.349	1.125
13	-1.08	0.313	-0.41	0.488
14	0.037	0.452	-0.174	-0.596
15	-0.643	0.456	-0.238	0.104
16	-0.349	0.149	0.057	0.072

Standard thresholds

P-value	Threshold
0.001	2.91381
0.0005	4.37276
0.0001	7.05446