SOX3.H12INVIVO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H12INVIVO.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	hddddbMATTGWbnnn
GC content	40.14%
Information content (bits; total / per base)	11.319 / 0.707
Data sources	HT-SELEX
Aligned words	2499

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)	0.642	0.664	0.463	0.526	0.649	0.692	1.619	1.788	14.824	32.523
Mouse	3 (11)	0.688	0.711	0.537	0.554	0.637	0.672	1.637	1.763	48.229	80.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.988	0.983	0.975	0.964	0.943	0.927
Overall, 2 experiments	best	0.997	0.996	0.99	0.986	0.966	0.957
Methyl HT-SELEX, 1 experiments	median	0.98	0.97	0.961	0.943	0.92	0.897
Methyl HT-SELEX, 1 experiments	best	0.98	0.97	0.961	0.943	0.92	0.897
Non-Methyl HT-SELEX, 1 experiments	median	0.997	0.996	0.99	0.986	0.966	0.957
Non-Methyl HT-SELEX, 1 experiments	best	0.997	0.996	0.99	0.986	0.966	0.957

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.673	0.346	0.553	0.461

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

PCM	SOX3.H12INVIVO.1.S.C.pcm
PWM	SOX3.H12INVIVO.1.S.C.pwm
PFM	SOX3.H12INVIVO.1.S.C.pfm
Alignment	SOX3.H12INVIVO.1.S.C.words.tsv
Threshold to P-value map	SOX3.H12INVIVO.1.S.C.thr
Motif in other formats
JASPAR format	SOX3.H12INVIVO.1.S.C_jaspar_format.txt
MEME format	SOX3.H12INVIVO.1.S.C_meme_format.meme
Transfac format	SOX3.H12INVIVO.1.S.C_transfac_format.txt
Homer format	SOX3.H12INVIVO.1.S.C_homer_format_0.001.txt SOX3.H12INVIVO.1.S.C_homer_format_0.0005.txt SOX3.H12INVIVO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	830.5	971.5	321.5	375.5
02	1477.75	279.75	287.75	453.75
03	1266.0	187.0	318.0	728.0
04	309.0	264.0	513.0	1413.0
05	518.0	314.0	1129.0	538.0
06	344.0	1149.0	555.0	451.0
07	535.0	1640.0	7.0	317.0
08	2485.0	9.0	5.0	0.0
09	1.0	1.0	4.0	2493.0
10	2.0	1.0	1.0	2495.0
11	6.0	10.0	2482.0	1.0
12	564.0	130.0	15.0	1790.0
13	217.0	828.0	475.0	979.0
14	673.0	877.0	545.0	404.0
15	381.0	881.0	508.0	729.0
16	491.25	703.25	637.25	667.25

PFM

	A	C	G	T
01	0.332	0.389	0.129	0.15
02	0.591	0.112	0.115	0.182
03	0.507	0.075	0.127	0.291
04	0.124	0.106	0.205	0.565
05	0.207	0.126	0.452	0.215
06	0.138	0.46	0.222	0.18
07	0.214	0.656	0.003	0.127
08	0.994	0.004	0.002	0.0
09	0.0	0.0	0.002	0.998
10	0.001	0.0	0.0	0.998
11	0.002	0.004	0.993	0.0
12	0.226	0.052	0.006	0.716
13	0.087	0.331	0.19	0.392
14	0.269	0.351	0.218	0.162
15	0.152	0.353	0.203	0.292
16	0.197	0.281	0.255	0.267

PWM

	A	C	G	T
01	0.284	0.44	-0.661	-0.507
02	0.859	-0.8	-0.772	-0.319
03	0.705	-1.199	-0.672	0.153
04	-0.701	-0.857	-0.196	0.814
05	-0.187	-0.685	0.59	-0.149
06	-0.594	0.608	-0.118	-0.325
07	-0.155	0.963	-4.248	-0.675
08	1.378	-4.047	-4.501	-5.77
09	-5.357	-5.357	-4.656	1.382
10	-5.065	-5.357	-5.357	1.382
11	-4.367	-3.959	1.377	-5.357
12	-0.102	-1.558	-3.61	1.051
13	-1.052	0.281	-0.273	0.448
14	0.074	0.338	-0.136	-0.434
15	-0.493	0.343	-0.206	0.154
16	-0.24	0.118	0.02	0.066

Standard thresholds

P-value	Threshold
0.001	4.36496
0.0005	5.60501
0.0001	7.53736