SOX7.H12RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX7.H12RSNP.1.SM.B
Gene (human)	SOX7 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox7
Gene synonyms (mouse)	Sox-7
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	17
Consensus	nvMMAWWdnCATTGTbn
GC content	32.86%
Information content (bits; total / per base)	15.5 / 0.912
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9938

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)	0.663	0.714	0.498	0.55	0.616	0.65	1.486	1.648	43.602	90.187

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.999	0.999	0.994	0.992	0.947	0.942
Overall, 3 experiments	best	1.0	1.0	0.997	0.996	0.949	0.947
Methyl HT-SELEX, 1 experiments	median	1.0	1.0	0.997	0.996	0.949	0.947
Methyl HT-SELEX, 1 experiments	best	1.0	1.0	0.997	0.996	0.949	0.947
Non-Methyl HT-SELEX, 2 experiments	median	0.818	0.821	0.784	0.785	0.745	0.745
Non-Methyl HT-SELEX, 2 experiments	best	0.999	0.999	0.994	0.992	0.947	0.942

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.715	0.529	0.585	0.415
batch 2	0.872	0.694	0.861	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.1.SM.B.pcm
PWM	SOX7.H12RSNP.1.SM.B.pwm
PFM	SOX7.H12RSNP.1.SM.B.pfm
Alignment	SOX7.H12RSNP.1.SM.B.words.tsv
Threshold to P-value map	SOX7.H12RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	SOX7.H12RSNP.1.SM.B_jaspar_format.txt
MEME format	SOX7.H12RSNP.1.SM.B_meme_format.meme
Transfac format	SOX7.H12RSNP.1.SM.B_transfac_format.txt
Homer format	SOX7.H12RSNP.1.SM.B_homer_format_0.001.txt SOX7.H12RSNP.1.SM.B_homer_format_0.0005.txt SOX7.H12RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3627.25	2169.25	2566.25	1575.25
02	5137.75	2064.75	1748.75	986.75
03	6824.0	2141.0	270.0	703.0
04	2904.0	6149.0	396.0	489.0
05	8425.0	222.0	218.0	1073.0
06	6663.0	321.0	335.0	2619.0
07	1064.0	497.0	898.0	7479.0
08	2518.0	726.0	1248.0	5446.0
09	2041.0	2810.0	2778.0	2309.0
10	638.0	7958.0	3.0	1339.0
11	9936.0	0.0	0.0	2.0
12	1.0	0.0	166.0	9771.0
13	0.0	0.0	4.0	9934.0
14	15.0	243.0	9680.0	0.0
15	565.0	89.0	71.0	9213.0
16	1085.75	2524.75	1633.75	4693.75
17	2208.75	3593.75	1984.75	2150.75

PFM

	A	C	G	T
01	0.365	0.218	0.258	0.159
02	0.517	0.208	0.176	0.099
03	0.687	0.215	0.027	0.071
04	0.292	0.619	0.04	0.049
05	0.848	0.022	0.022	0.108
06	0.67	0.032	0.034	0.264
07	0.107	0.05	0.09	0.753
08	0.253	0.073	0.126	0.548
09	0.205	0.283	0.28	0.232
10	0.064	0.801	0.0	0.135
11	1.0	0.0	0.0	0.0
12	0.0	0.0	0.017	0.983
13	0.0	0.0	0.0	1.0
14	0.002	0.024	0.974	0.0
15	0.057	0.009	0.007	0.927
16	0.109	0.254	0.164	0.472
17	0.222	0.362	0.2	0.216

PWM

	A	C	G	T
01	0.378	-0.136	0.032	-0.455
02	0.726	-0.185	-0.351	-0.922
03	1.01	-0.149	-2.212	-1.26
04	0.156	0.906	-1.832	-1.622
05	1.22	-2.406	-2.424	-0.838
06	0.986	-2.04	-1.998	0.053
07	-0.847	-1.606	-1.016	1.101
08	0.013	-1.228	-0.688	0.784
09	-0.196	0.123	0.112	-0.073
10	-1.357	1.163	-6.151	-0.617
11	1.385	-6.985	-6.985	-6.36
12	-6.625	-6.985	-2.693	1.369
13	-6.985	-6.985	-5.978	1.385
14	-4.968	-2.316	1.359	-6.985
15	-1.478	-3.305	-3.524	1.31
16	-0.827	0.016	-0.419	0.636
17	-0.118	0.369	-0.224	-0.144

Standard thresholds

P-value	Threshold
0.001	1.95306
0.0005	3.43941
0.0001	6.36481