SOX7.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX7.H12INVITRO.0.PS.A
Gene (human)	SOX7 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox7
Gene synonyms (mouse)	Sox-7
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	ndMATTGWd
GC content	38.31%
Information content (bits; total / per base)	8.266 / 0.918
Data sources	ChIP-Seq + HT-SELEX
Aligned words	4500

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
Mouse	1 (5)	0.694	0.733	0.535	0.586	0.681	0.7	1.693	1.786	70.161	123.125

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.962	0.94	0.93	0.901	0.85	0.829
Overall, 3 experiments	best	0.976	0.962	0.947	0.926	0.854	0.838
Methyl HT-SELEX, 1 experiments	median	0.976	0.962	0.947	0.926	0.85	0.838
Methyl HT-SELEX, 1 experiments	best	0.976	0.962	0.947	0.926	0.85	0.838
Non-Methyl HT-SELEX, 2 experiments	median	0.794	0.774	0.752	0.733	0.701	0.686
Non-Methyl HT-SELEX, 2 experiments	best	0.962	0.94	0.93	0.901	0.854	0.829

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.658	0.455	0.501	0.323
batch 2	0.625	0.513	0.681	0.18

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 F {4.1.1.6} (TFClass)
TFClass ID	TFClass: 4.1.1.6.1
HGNC	HGNC:18196
MGI	MGI:98369
EntrezGene (human)	GeneID:83595 (SSTAR profile)
EntrezGene (mouse)	GeneID:20680 (SSTAR profile)
UniProt ID (human)	SOX7_HUMAN
UniProt ID (mouse)	SOX7_MOUSE
UniProt AC (human)	Q9BT81 (TFClass)
UniProt AC (mouse)	P40646 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	2
Methyl-HT-SELEX	1

PCM	SOX7.H12INVITRO.0.PS.A.pcm
PWM	SOX7.H12INVITRO.0.PS.A.pwm
PFM	SOX7.H12INVITRO.0.PS.A.pfm
Alignment	SOX7.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	SOX7.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	SOX7.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	SOX7.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	SOX7.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	SOX7.H12INVITRO.0.PS.A_homer_format_0.001.txt SOX7.H12INVITRO.0.PS.A_homer_format_0.0005.txt SOX7.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1162.5	966.5	775.5	1595.5
02	697.0	615.0	1262.0	1926.0
03	975.0	2611.0	280.0	634.0
04	4298.0	0.0	202.0	0.0
05	0.0	0.0	1910.0	2590.0
06	0.0	0.0	228.0	4272.0
07	11.0	0.0	4489.0	0.0
08	483.75	191.75	329.75	3494.75
09	680.0	288.0	1366.0	2166.0

PFM

	A	C	G	T
01	0.258	0.215	0.172	0.355
02	0.155	0.137	0.28	0.428
03	0.217	0.58	0.062	0.141
04	0.955	0.0	0.045	0.0
05	0.0	0.0	0.424	0.576
06	0.0	0.0	0.051	0.949
07	0.002	0.0	0.998	0.0
08	0.108	0.043	0.073	0.777
09	0.151	0.064	0.304	0.481

PWM

	A	C	G	T
01	0.033	-0.152	-0.371	0.349
02	-0.478	-0.602	0.115	0.537
03	-0.143	0.841	-1.385	-0.572
04	1.339	-6.284	-1.709	-6.284
05	-6.284	-6.284	0.529	0.833
06	-6.284	-6.284	-1.589	1.333
07	-4.455	-6.284	1.382	-6.284
08	-0.841	-1.76	-1.223	1.132
09	-0.502	-1.357	0.194	0.654

Standard thresholds

P-value	Threshold
0.001	5.32557
0.0005	6.02676
0.0001	7.189945