SOX3.H12INVITRO.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H12INVITRO.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	14
Consensus	hddddbMATTGWbn
GC content	37.94%
Information content (bits; total / per base)	10.659 / 0.761
Data sources	HT-SELEX
Aligned words	9973

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)	0.639	0.663	0.452	0.501	0.647	0.682	1.596	1.711	11.056	27.398
Mouse	3 (11)	0.679	0.708	0.515	0.541	0.622	0.663	1.544	1.694	38.161	64.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.988	0.983	0.975	0.963	0.943	0.926
Overall, 2 experiments	best	0.998	0.997	0.991	0.987	0.967	0.959
Methyl HT-SELEX, 1 experiments	median	0.979	0.969	0.958	0.94	0.918	0.893
Methyl HT-SELEX, 1 experiments	best	0.979	0.969	0.958	0.94	0.918	0.893
Non-Methyl HT-SELEX, 1 experiments	median	0.998	0.997	0.991	0.987	0.967	0.959
Non-Methyl HT-SELEX, 1 experiments	best	0.998	0.997	0.991	0.987	0.967	0.959

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.661	0.336	0.537	0.448

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.H12INVITRO.1.S.C.pcm
PWM	SOX3.H12INVITRO.1.S.C.pwm
PFM	SOX3.H12INVITRO.1.S.C.pfm
Alignment	SOX3.H12INVITRO.1.S.C.words.tsv
Threshold to P-value map	SOX3.H12INVITRO.1.S.C.thr
Motif in other formats
JASPAR format	SOX3.H12INVITRO.1.S.C_jaspar_format.txt
MEME format	SOX3.H12INVITRO.1.S.C_meme_format.meme
Transfac format	SOX3.H12INVITRO.1.S.C_transfac_format.txt
Homer format	SOX3.H12INVITRO.1.S.C_homer_format_0.001.txt SOX3.H12INVITRO.1.S.C_homer_format_0.0005.txt SOX3.H12INVITRO.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3179.5	3648.5	1500.5	1644.5
02	5696.5	1156.5	1355.5	1764.5
03	5056.0	778.0	1291.0	2848.0
04	1331.0	1131.0	1860.0	5651.0
05	2165.0	1231.0	4572.0	2005.0
06	1383.0	3979.0	2488.0	2123.0
07	2060.0	6548.0	67.0	1298.0
08	9937.0	23.0	8.0	5.0
09	4.0	2.0	9.0	9958.0
10	1.0	14.0	10.0	9948.0
11	57.0	181.0	9734.0	1.0
12	2643.0	723.0	158.0	6449.0
13	1078.25	2774.25	2245.25	3875.25
14	2293.25	3000.25	2490.25	2189.25

PFM

	A	C	G	T
01	0.319	0.366	0.15	0.165
02	0.571	0.116	0.136	0.177
03	0.507	0.078	0.129	0.286
04	0.133	0.113	0.187	0.567
05	0.217	0.123	0.458	0.201
06	0.139	0.399	0.249	0.213
07	0.207	0.657	0.007	0.13
08	0.996	0.002	0.001	0.001
09	0.0	0.0	0.001	0.998
10	0.0	0.001	0.001	0.997
11	0.006	0.018	0.976	0.0
12	0.265	0.072	0.016	0.647
13	0.108	0.278	0.225	0.389
14	0.23	0.301	0.25	0.22

PWM

	A	C	G	T
01	0.243	0.38	-0.507	-0.416
02	0.826	-0.767	-0.609	-0.345
03	0.707	-1.163	-0.657	0.133
04	-0.627	-0.789	-0.293	0.818
05	-0.141	-0.705	0.606	-0.218
06	-0.589	0.467	-0.002	-0.161
07	-0.191	0.965	-3.584	-0.652
08	1.382	-4.591	-5.49	-5.834
09	-5.981	-6.363	-5.397	1.384
10	-6.628	-5.031	-5.313	1.383
11	-3.74	-2.611	1.361	-6.628
12	0.058	-1.236	-2.745	0.95
13	-0.837	0.107	-0.105	0.441
14	-0.084	0.185	-0.001	-0.13

Standard thresholds

P-value	Threshold
0.001	4.73596
0.0005	5.81586
0.0001	7.53951