SOX8.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX8.H12INVIVO.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	17
Consensus	hvMRddvnnbYWTTGTb
GC content	40.37%
Information content (bits; total / per base)	11.457 / 0.674
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	999

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)	0.789	0.842	0.734	0.787	0.78	0.838	2.919	3.237	129.444	179.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.985	0.979	0.958	0.947	0.901	0.895
Overall, 4 experiments	best	1.0	1.0	1.0	1.0	0.999	0.998
Methyl HT-SELEX, 2 experiments	median	0.985	0.979	0.958	0.947	0.903	0.897
Methyl HT-SELEX, 2 experiments	best	1.0	1.0	1.0	1.0	0.999	0.998
Non-Methyl HT-SELEX, 2 experiments	median	0.974	0.965	0.932	0.92	0.868	0.865
Non-Methyl HT-SELEX, 2 experiments	best	1.0	1.0	0.999	0.999	0.994	0.993

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.721	0.436	0.609	0.424

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.H12INVIVO.0.PSM.A.pcm
PWM	SOX8.H12INVIVO.0.PSM.A.pwm
PFM	SOX8.H12INVIVO.0.PSM.A.pfm
Alignment	SOX8.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SOX8.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX8.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SOX8.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SOX8.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SOX8.H12INVIVO.0.PSM.A_homer_format_0.001.txt SOX8.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SOX8.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	531.0	179.0	77.0	212.0
02	403.0	336.0	143.0	117.0
03	763.0	154.0	46.0	36.0
04	736.0	59.0	135.0	69.0
05	450.0	54.0	227.0	268.0
06	357.0	98.0	408.0	136.0
07	290.25	172.25	430.25	106.25
08	292.25	257.25	298.25	151.25
09	157.25	293.25	307.25	241.25
10	62.25	453.25	214.25	269.25
11	56.25	775.25	35.25	132.25
12	499.25	45.25	8.25	446.25
13	7.25	129.25	59.25	803.25
14	1.25	14.25	4.25	979.25
15	23.25	30.25	942.25	3.25
16	8.25	7.25	7.25	976.25
17	50.25	226.25	230.25	492.25

PFM

	A	C	G	T
01	0.532	0.179	0.077	0.212
02	0.403	0.336	0.143	0.117
03	0.764	0.154	0.046	0.036
04	0.737	0.059	0.135	0.069
05	0.45	0.054	0.227	0.268
06	0.357	0.098	0.408	0.136
07	0.291	0.172	0.431	0.106
08	0.293	0.258	0.299	0.151
09	0.157	0.294	0.308	0.241
10	0.062	0.454	0.214	0.27
11	0.056	0.776	0.035	0.132
12	0.5	0.045	0.008	0.447
13	0.007	0.129	0.059	0.804
14	0.001	0.014	0.004	0.98
15	0.023	0.03	0.943	0.003
16	0.008	0.007	0.007	0.977
17	0.05	0.226	0.23	0.493

PWM

	A	C	G	T
01	0.751	-0.33	-1.161	-0.163
02	0.476	0.295	-0.553	-0.751
03	1.112	-0.479	-1.662	-1.897
04	1.076	-1.421	-0.609	-1.269
05	0.586	-1.507	-0.095	0.07
06	0.355	-0.925	0.488	-0.602
07	0.149	-0.368	0.541	-0.845
08	0.156	0.029	0.176	-0.497
09	-0.459	0.16	0.206	-0.034
10	-1.369	0.593	-0.152	0.075
11	-1.467	1.128	-1.917	-0.63
12	0.689	-1.678	-3.227	0.577
13	-3.333	-0.652	-1.417	1.163
14	-4.437	-2.756	-3.739	1.361
15	-2.309	-2.062	1.323	-3.923
16	-3.227	-3.333	-3.333	1.358
17	-1.577	-0.098	-0.081	0.675

Standard thresholds

P-value	Threshold
0.001	4.37546
0.0005	5.31701
0.0001	7.22996