SOX8.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX8.H12INVITRO.0.PSM.A
Gene (human)	SOX8 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox8
Gene synonyms (mouse)	Sox-8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	18
Consensus	hMWWddbSYATTGTTYhn
GC content	35.21%
Information content (bits; total / per base)	16.98 / 0.943
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	746

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)	0.686	0.722	0.543	0.576	0.655	0.71	1.849	2.07	62.481	78.469

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.996	0.994	0.989	0.985	0.959	0.952
Overall, 4 experiments	best	0.998	0.997	0.997	0.995	0.993	0.989
Methyl HT-SELEX, 2 experiments	median	0.997	0.996	0.991	0.987	0.962	0.956
Methyl HT-SELEX, 2 experiments	best	0.998	0.997	0.997	0.995	0.993	0.989
Non-Methyl HT-SELEX, 2 experiments	median	0.99	0.985	0.964	0.955	0.886	0.888
Non-Methyl HT-SELEX, 2 experiments	best	0.997	0.994	0.994	0.99	0.986	0.98

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.745	0.412	0.66	0.44

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.0.PSM.A.pcm
PWM	SOX8.H12INVITRO.0.PSM.A.pwm
PFM	SOX8.H12INVITRO.0.PSM.A.pfm
Alignment	SOX8.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SOX8.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX8.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SOX8.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SOX8.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SOX8.H12INVITRO.0.PSM.A_homer_format_0.001.txt SOX8.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SOX8.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	384.0	239.0	46.0	77.0
02	416.0	242.0	25.0	63.0
03	509.0	53.0	26.0	158.0
04	329.0	17.0	74.0	326.0
05	190.0	28.0	232.0	296.0
06	196.0	79.0	321.0	150.0
07	65.0	193.0	312.0	176.0
08	9.0	559.0	92.0	86.0
09	17.0	282.0	2.0	445.0
10	742.0	0.0	0.0	4.0
11	0.0	0.0	0.0	746.0
12	0.0	0.0	0.0	746.0
13	0.0	0.0	746.0	0.0
14	0.0	0.0	0.0	746.0
15	11.0	19.0	2.0	714.0
16	103.0	505.0	26.0	112.0
17	132.75	143.75	127.75	341.75
18	168.75	213.75	122.75	240.75

PFM

	A	C	G	T
01	0.515	0.32	0.062	0.103
02	0.558	0.324	0.034	0.084
03	0.682	0.071	0.035	0.212
04	0.441	0.023	0.099	0.437
05	0.255	0.038	0.311	0.397
06	0.263	0.106	0.43	0.201
07	0.087	0.259	0.418	0.236
08	0.012	0.749	0.123	0.115
09	0.023	0.378	0.003	0.597
10	0.995	0.0	0.0	0.005
11	0.0	0.0	0.0	1.0
12	0.0	0.0	0.0	1.0
13	0.0	0.0	1.0	0.0
14	0.0	0.0	0.0	1.0
15	0.015	0.025	0.003	0.957
16	0.138	0.677	0.035	0.15
17	0.178	0.193	0.171	0.458
18	0.226	0.287	0.165	0.323

PWM

	A	C	G	T
01	0.718	0.246	-1.373	-0.872
02	0.797	0.258	-1.954	-1.068
03	0.998	-1.236	-1.918	-0.164
04	0.564	-2.311	-0.911	0.555
05	0.018	-1.848	0.217	0.459
06	0.049	-0.847	0.539	-0.216
07	-1.038	0.034	0.511	-0.057
08	-2.871	1.092	-0.698	-0.764
09	-2.311	0.41	-3.942	0.865
10	1.374	-4.734	-4.734	-3.505
11	-4.734	-4.734	-4.734	1.38
12	-4.734	-4.734	-4.734	1.38
13	-4.734	-4.734	1.38	-4.734
14	-4.734	-4.734	-4.734	1.38
15	-2.699	-2.209	-3.942	1.336
16	-0.587	0.991	-1.918	-0.504
17	-0.336	-0.258	-0.374	0.602
18	-0.099	0.135	-0.414	0.253

Standard thresholds

P-value	Threshold
0.001	1.09496
0.0005	2.59556
0.0001	5.68706