SOX4.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX4.H12CORE.0.PSM.A
Gene (human)	SOX4 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox4
Gene synonyms (mouse)	Sox-4
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	nbYCTTTGTTYbn
GC content	45.38%
Information content (bits; total / per base)	13.818 / 1.063
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8290

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	10 (58)	0.658	0.935	0.581	0.881	0.693	0.945	2.364	3.987	35.251	233.201
Mouse	4 (26)	0.815	0.886	0.74	0.821	0.853	0.918	3.512	4.113	227.423	431.081

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.994	0.99	0.991	0.985	0.981	0.973
Overall, 2 experiments	best	0.995	0.992	0.992	0.988	0.985	0.977
Methyl HT-SELEX, 1 experiments	median	0.993	0.988	0.989	0.982	0.978	0.968
Methyl HT-SELEX, 1 experiments	best	0.993	0.988	0.989	0.982	0.978	0.968
Non-Methyl HT-SELEX, 1 experiments	median	0.995	0.992	0.992	0.988	0.985	0.977
Non-Methyl HT-SELEX, 1 experiments	best	0.995	0.992	0.992	0.988	0.985	0.977

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 C {4.1.1.3} (TFClass)
TFClass ID	TFClass: 4.1.1.3.1
HGNC	HGNC:11200
MGI	MGI:98366
EntrezGene (human)	GeneID:6659 (SSTAR profile)
EntrezGene (mouse)	GeneID:20677 (SSTAR profile)
UniProt ID (human)	SOX4_HUMAN
UniProt ID (mouse)	SOX4_MOUSE
UniProt AC (human)	Q06945 (TFClass)
UniProt AC (mouse)	Q06831 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	10 human, 4 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	SOX4.H12CORE.0.PSM.A.pcm
PWM	SOX4.H12CORE.0.PSM.A.pwm
PFM	SOX4.H12CORE.0.PSM.A.pfm
Alignment	SOX4.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	SOX4.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX4.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	SOX4.H12CORE.0.PSM.A_meme_format.meme
Transfac format	SOX4.H12CORE.0.PSM.A_transfac_format.txt
Homer format	SOX4.H12CORE.0.PSM.A_homer_format_0.001.txt SOX4.H12CORE.0.PSM.A_homer_format_0.0005.txt SOX4.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1683.5	2002.5	2550.5	2053.5
02	384.0	3416.0	2046.0	2444.0
03	13.0	5858.0	831.0	1588.0
04	0.0	7584.0	1.0	705.0
05	1965.0	0.0	0.0	6325.0
06	0.0	0.0	0.0	8290.0
07	0.0	0.0	0.0	8290.0
08	0.0	0.0	8290.0	0.0
09	0.0	0.0	0.0	8290.0
10	23.0	1455.0	126.0	6686.0
11	969.0	5449.0	556.0	1316.0
12	804.5	2349.5	2053.5	3082.5
13	1502.25	2676.25	1660.25	2451.25

PFM

	A	C	G	T
01	0.203	0.242	0.308	0.248
02	0.046	0.412	0.247	0.295
03	0.002	0.707	0.1	0.192
04	0.0	0.915	0.0	0.085
05	0.237	0.0	0.0	0.763
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	1.0	0.0
09	0.0	0.0	0.0	1.0
10	0.003	0.176	0.015	0.807
11	0.117	0.657	0.067	0.159
12	0.097	0.283	0.248	0.372
13	0.181	0.323	0.2	0.296

PWM

	A	C	G	T
01	-0.208	-0.034	0.207	-0.009
02	-1.681	0.499	-0.013	0.165
03	-4.913	1.038	-0.912	-0.266
04	-6.824	1.296	-6.457	-1.076
05	-0.053	-6.824	-6.824	1.115
06	-6.824	-6.824	-6.824	1.385
07	-6.824	-6.824	-6.824	1.385
08	-6.824	-6.824	1.385	-6.824
09	-6.824	-6.824	-6.824	1.385
10	-4.409	-0.353	-2.784	1.171
11	-0.759	0.966	-1.313	-0.454
12	-0.945	0.125	-0.009	0.397
13	-0.321	0.255	-0.222	0.168

Standard thresholds

P-value	Threshold
0.001	0.987315
0.0005	2.84416
0.0001	7.143535