SOX3.H12INVITRO.0.PM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX3.H12INVITRO.0.PM.A
Gene (human)	SOX3 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox3
Gene synonyms (mouse)	Sox-3
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nnSYATTGTYhn
GC content	38.32%
Information content (bits; total / per base)	12.05 / 1.004
Data sources	ChIP-Seq + Methyl-HT-SELEX
Aligned words	9983

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)	0.728	0.752	0.556	0.582	0.76	0.786	2.038	2.184	13.678	48.553
Mouse	3 (11)	0.799	0.818	0.639	0.677	0.799	0.814	2.346	2.465	81.796	164.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.979	0.965	0.969	0.95	0.928	0.908
Overall, 2 experiments	best	0.988	0.979	0.981	0.97	0.959	0.943
Methyl HT-SELEX, 1 experiments	median	0.988	0.979	0.981	0.97	0.959	0.943
Methyl HT-SELEX, 1 experiments	best	0.988	0.979	0.981	0.97	0.959	0.943
Non-Methyl HT-SELEX, 1 experiments	median	0.97	0.951	0.956	0.931	0.897	0.872
Non-Methyl HT-SELEX, 1 experiments	best	0.97	0.951	0.956	0.931	0.897	0.872

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.596	0.296	0.523	0.383

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.0.PM.A.pcm
PWM	SOX3.H12INVITRO.0.PM.A.pwm
PFM	SOX3.H12INVITRO.0.PM.A.pfm
Alignment	SOX3.H12INVITRO.0.PM.A.words.tsv
Threshold to P-value map	SOX3.H12INVITRO.0.PM.A.thr
Motif in other formats
JASPAR format	SOX3.H12INVITRO.0.PM.A_jaspar_format.txt
MEME format	SOX3.H12INVITRO.0.PM.A_meme_format.meme
Transfac format	SOX3.H12INVITRO.0.PM.A_transfac_format.txt
Homer format	SOX3.H12INVITRO.0.PM.A_homer_format_0.001.txt SOX3.H12INVITRO.0.PM.A_homer_format_0.0005.txt SOX3.H12INVITRO.0.PM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2125.25	1928.25	2407.25	3522.25
02	1363.0	2656.0	2989.0	2975.0
03	331.0	6196.0	2137.0	1319.0
04	287.0	5073.0	23.0	4600.0
05	9835.0	3.0	0.0	145.0
06	1.0	0.0	0.0	9982.0
07	0.0	0.0	0.0	9983.0
08	0.0	2.0	9981.0	0.0
09	14.0	0.0	1.0	9968.0
10	581.0	2482.0	820.0	6100.0
11	2498.25	3935.25	1054.25	2495.25
12	2154.75	2518.75	1699.75	3609.75

PFM

	A	C	G	T
01	0.213	0.193	0.241	0.353
02	0.137	0.266	0.299	0.298
03	0.033	0.621	0.214	0.132
04	0.029	0.508	0.002	0.461
05	0.985	0.0	0.0	0.015
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.001	0.0	0.0	0.998
10	0.058	0.249	0.082	0.611
11	0.25	0.394	0.106	0.25
12	0.216	0.252	0.17	0.362

PWM

	A	C	G	T
01	-0.161	-0.258	-0.036	0.344
02	-0.604	0.062	0.18	0.176
03	-2.014	0.909	-0.155	-0.637
04	-2.156	0.709	-4.592	0.611
05	1.371	-6.155	-6.989	-2.831
06	-6.629	-6.989	-6.989	1.386
07	-6.989	-6.989	-6.989	1.386
08	-6.989	-6.364	1.385	-6.989
09	-5.032	-6.989	-6.629	1.384
10	-1.455	-0.006	-1.111	0.893
11	0.001	0.455	-0.861	-0.0
12	-0.147	0.009	-0.384	0.369

Standard thresholds

P-value	Threshold
0.001	2.444595
0.0005	4.778575
0.0001	7.812235