SOX8.H12INVITRO.1.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX8.H12INVITRO.1.PS.A
Gene (human)	SOX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox8
Gene synonyms (mouse)	Sox-8
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	11
Consensus	nbYATTGTYhn
GC content	36.58%
Information content (bits; total / per base)	11.82 / 1.075
Data sources	ChIP-Seq + HT-SELEX
Aligned words	9912

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	3 (15)	0.678	0.71	0.531	0.562	0.636	0.681	1.623	1.817	57.62	80.051

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.993	0.988	0.987	0.98	0.968	0.957
Overall, 4 experiments	best	0.995	0.992	0.993	0.988	0.989	0.983
Methyl HT-SELEX, 2 experiments	median	0.993	0.988	0.988	0.981	0.971	0.961
Methyl HT-SELEX, 2 experiments	best	0.995	0.991	0.993	0.988	0.989	0.983
Non-Methyl HT-SELEX, 2 experiments	median	0.987	0.979	0.965	0.953	0.894	0.891
Non-Methyl HT-SELEX, 2 experiments	best	0.995	0.992	0.992	0.987	0.983	0.976

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.771	0.447	0.69	0.472

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 E {4.1.1.5} (TFClass)
TFClass ID	TFClass: 4.1.1.5.1
HGNC	HGNC:11203
MGI	MGI:98370
EntrezGene (human)	GeneID:30812 (SSTAR profile)
EntrezGene (mouse)	GeneID:20681 (SSTAR profile)
UniProt ID (human)	SOX8_HUMAN
UniProt ID (mouse)	SOX8_MOUSE
UniProt AC (human)	P57073 (TFClass)
UniProt AC (mouse)	Q04886 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	3 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	SOX8.H12INVITRO.1.PS.A.pcm
PWM	SOX8.H12INVITRO.1.PS.A.pwm
PFM	SOX8.H12INVITRO.1.PS.A.pfm
Alignment	SOX8.H12INVITRO.1.PS.A.words.tsv
Threshold to P-value map	SOX8.H12INVITRO.1.PS.A.thr
Motif in other formats
JASPAR format	SOX8.H12INVITRO.1.PS.A_jaspar_format.txt
MEME format	SOX8.H12INVITRO.1.PS.A_meme_format.meme
Transfac format	SOX8.H12INVITRO.1.PS.A_transfac_format.txt
Homer format	SOX8.H12INVITRO.1.PS.A_homer_format_0.001.txt SOX8.H12INVITRO.1.PS.A_homer_format_0.0005.txt SOX8.H12INVITRO.1.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1850.0	2394.0	3035.0	2633.0
02	581.0	5539.0	2164.0	1628.0
03	884.0	4670.0	337.0	4021.0
04	9815.0	5.0	6.0	86.0
05	0.0	0.0	0.0	9912.0
06	0.0	0.0	0.0	9912.0
07	0.0	0.0	9912.0	0.0
08	9.0	0.0	0.0	9903.0
09	844.0	1351.0	513.0	7204.0
10	1530.5	4596.5	922.5	2862.5
11	1930.75	2164.75	2268.75	3547.75

PFM

	A	C	G	T
01	0.187	0.242	0.306	0.266
02	0.059	0.559	0.218	0.164
03	0.089	0.471	0.034	0.406
04	0.99	0.001	0.001	0.009
05	0.0	0.0	0.0	1.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	1.0	0.0
08	0.001	0.0	0.0	0.999
09	0.085	0.136	0.052	0.727
10	0.154	0.464	0.093	0.289
11	0.195	0.218	0.229	0.358

PWM

	A	C	G	T
01	-0.292	-0.034	0.203	0.061
02	-1.447	0.804	-0.135	-0.42
03	-1.029	0.633	-1.989	0.484
04	1.376	-5.828	-5.7	-3.335
05	-6.983	-6.983	-6.983	1.386
06	-6.983	-6.983	-6.983	1.386
07	-6.983	-6.983	1.386	-6.983
08	-5.391	-6.983	-6.983	1.385
09	-1.075	-0.606	-1.571	1.067
10	-0.481	0.617	-0.987	0.144
11	-0.249	-0.135	-0.088	0.359

Standard thresholds

P-value	Threshold
0.001	2.97671
0.0005	5.318535
0.0001	7.720545