SOX7.H12RSNP.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX7.H12RSNP.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	YCATTGTYY
GC content	39.18%
Information content (bits; total / per base)	11.761 / 1.307
Data sources	ChIP-Seq + HT-SELEX
Aligned words	985

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)	0.813	0.869	0.78	0.845	0.814	0.857	3.166	3.495	168.481	347.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.959	0.936	0.912	0.883	0.801	0.793
Overall, 3 experiments	best	0.966	0.946	0.922	0.896	0.81	0.793
Methyl HT-SELEX, 1 experiments	median	0.966	0.946	0.922	0.896	0.801	0.793
Methyl HT-SELEX, 1 experiments	best	0.966	0.946	0.922	0.896	0.801	0.793
Non-Methyl HT-SELEX, 2 experiments	median	0.772	0.748	0.733	0.711	0.672	0.66
Non-Methyl HT-SELEX, 2 experiments	best	0.959	0.936	0.912	0.883	0.81	0.793

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.67	0.52	0.527	0.313
batch 2	0.722	0.597	0.668	0.36

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.H12RSNP.0.PS.A.pcm
PWM	SOX7.H12RSNP.0.PS.A.pwm
PFM	SOX7.H12RSNP.0.PS.A.pfm
Alignment	SOX7.H12RSNP.0.PS.A.words.tsv
Threshold to P-value map	SOX7.H12RSNP.0.PS.A.thr
Motif in other formats
JASPAR format	SOX7.H12RSNP.0.PS.A_jaspar_format.txt
MEME format	SOX7.H12RSNP.0.PS.A_meme_format.meme
Transfac format	SOX7.H12RSNP.0.PS.A_transfac_format.txt
Homer format	SOX7.H12RSNP.0.PS.A_homer_format_0.001.txt SOX7.H12RSNP.0.PS.A_homer_format_0.0005.txt SOX7.H12RSNP.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	17.0	745.0	88.0	135.0
02	16.0	733.0	9.0	227.0
03	880.0	17.0	3.0	85.0
04	5.0	8.0	18.0	954.0
05	9.0	5.0	2.0	969.0
06	9.0	17.0	883.0	76.0
07	6.0	8.0	9.0	962.0
08	14.0	242.0	36.0	693.0
09	33.0	611.0	39.0	302.0

PFM

	A	C	G	T
01	0.017	0.756	0.089	0.137
02	0.016	0.744	0.009	0.23
03	0.893	0.017	0.003	0.086
04	0.005	0.008	0.018	0.969
05	0.009	0.005	0.002	0.984
06	0.009	0.017	0.896	0.077
07	0.006	0.008	0.009	0.977
08	0.014	0.246	0.037	0.704
09	0.034	0.62	0.04	0.307

PWM

	A	C	G	T
01	-2.584	1.102	-1.017	-0.595
02	-2.638	1.086	-3.141	-0.081
03	1.269	-2.584	-3.961	-1.051
04	-3.608	-3.239	-2.532	1.349
05	-3.141	-3.608	-4.199	1.365
06	-3.141	-2.584	1.272	-1.16
07	-3.469	-3.239	-3.141	1.357
08	-2.758	-0.017	-1.883	1.03
09	-1.966	0.905	-1.807	0.203

Standard thresholds

P-value	Threshold
0.001	4.118705
0.0005	5.17094
0.0001	7.21355