SOX4.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX4.H12INVIVO.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	11
Consensus	bYCTTTGTYYb
GC content	44.76%
Information content (bits; total / per base)	11.855 / 1.078
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	1007

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)	0.65	0.923	0.58	0.873	0.697	0.936	2.421	4.025	35.676	252.824
Mouse	4 (26)	0.805	0.887	0.734	0.82	0.856	0.922	3.561	4.146	227.421	445.854

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.994	0.99	0.989	0.983	0.976	0.967
Overall, 2 experiments	best	0.995	0.991	0.991	0.985	0.981	0.972
Methyl HT-SELEX, 1 experiments	median	0.992	0.988	0.987	0.98	0.972	0.961
Methyl HT-SELEX, 1 experiments	best	0.992	0.988	0.987	0.98	0.972	0.961
Non-Methyl HT-SELEX, 1 experiments	median	0.995	0.991	0.991	0.985	0.981	0.972
Non-Methyl HT-SELEX, 1 experiments	best	0.995	0.991	0.991	0.985	0.981	0.972

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.H12INVIVO.0.PSM.A.pcm
PWM	SOX4.H12INVIVO.0.PSM.A.pwm
PFM	SOX4.H12INVIVO.0.PSM.A.pfm
Alignment	SOX4.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	SOX4.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX4.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	SOX4.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	SOX4.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	SOX4.H12INVIVO.0.PSM.A_homer_format_0.001.txt SOX4.H12INVIVO.0.PSM.A_homer_format_0.0005.txt SOX4.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	44.0	371.0	284.0	308.0
02	7.0	496.0	174.0	330.0
03	3.0	881.0	7.0	116.0
04	142.0	7.0	9.0	849.0
05	3.0	15.0	7.0	982.0
06	2.0	10.0	8.0	987.0
07	8.0	27.0	961.0	11.0
08	3.0	10.0	11.0	983.0
09	17.0	280.0	135.0	575.0
10	33.0	653.0	75.0	246.0
11	89.0	324.0	213.0	381.0

PFM

	A	C	G	T
01	0.044	0.368	0.282	0.306
02	0.007	0.493	0.173	0.328
03	0.003	0.875	0.007	0.115
04	0.141	0.007	0.009	0.843
05	0.003	0.015	0.007	0.975
06	0.002	0.01	0.008	0.98
07	0.008	0.027	0.954	0.011
08	0.003	0.01	0.011	0.976
09	0.017	0.278	0.134	0.571
10	0.033	0.648	0.074	0.244
11	0.088	0.322	0.212	0.378

PWM

	A	C	G	T
01	-1.713	0.386	0.12	0.2
02	-3.369	0.675	-0.366	0.269
03	-3.982	1.248	-3.369	-0.767
04	-0.567	-3.369	-3.162	1.211
05	-3.982	-2.718	-3.369	1.356
06	-4.219	-3.073	-3.26	1.361
07	-3.26	-2.177	1.334	-2.991
08	-3.982	-3.073	-2.991	1.357
09	-2.605	0.106	-0.617	0.822
10	-1.988	0.949	-1.195	-0.023
11	-1.027	0.251	-0.166	0.412

Standard thresholds

P-value	Threshold
0.001	4.08798
0.0005	5.10193
0.0001	7.361265