SOX4.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX4.H12INVITRO.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	19
Consensus	hhhddddbCCTTTGTTYbn
GC content	40.49%
Information content (bits; total / per base)	15.93 / 0.838
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	562

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)	0.647	0.901	0.511	0.797	0.659	0.915	2.103	3.831	17.922	177.77
Mouse	4 (26)	0.78	0.86	0.637	0.76	0.8	0.892	2.964	3.753	130.659	309.092

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.995	0.991	0.991	0.986	0.98	0.972
Overall, 2 experiments	best	0.995	0.992	0.992	0.987	0.983	0.975
Methyl HT-SELEX, 1 experiments	median	0.994	0.99	0.99	0.985	0.977	0.968
Methyl HT-SELEX, 1 experiments	best	0.994	0.99	0.99	0.985	0.977	0.968
Non-Methyl HT-SELEX, 1 experiments	median	0.995	0.992	0.992	0.987	0.983	0.975
Non-Methyl HT-SELEX, 1 experiments	best	0.995	0.992	0.992	0.987	0.983	0.975

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.H12INVITRO.0.PSM.A.pcm
PWM	SOX4.H12INVITRO.0.PSM.A.pwm
PFM	SOX4.H12INVITRO.0.PSM.A.pfm
Alignment	SOX4.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SOX4.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SOX4.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SOX4.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SOX4.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SOX4.H12INVITRO.0.PSM.A_homer_format_0.001.txt SOX4.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SOX4.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	189.5	164.5	65.5	142.5
02	152.25	186.25	60.25	163.25
03	186.0	125.0	45.0	206.0
04	212.0	38.0	78.0	234.0
05	160.0	36.0	110.0	256.0
06	113.0	30.0	244.0	175.0
07	85.0	83.0	191.0	203.0
08	6.0	198.0	131.0	227.0
09	0.0	490.0	3.0	69.0
10	0.0	511.0	0.0	51.0
11	85.0	0.0	0.0	477.0
12	0.0	0.0	0.0	562.0
13	0.0	0.0	0.0	562.0
14	0.0	0.0	562.0	0.0
15	0.0	0.0	0.0	562.0
16	3.0	107.0	1.0	451.0
17	96.0	346.0	20.0	100.0
18	76.25	148.25	110.25	227.25
19	127.0	142.0	98.0	195.0

PFM

	A	C	G	T
01	0.337	0.293	0.117	0.254
02	0.271	0.331	0.107	0.29
03	0.331	0.222	0.08	0.367
04	0.377	0.068	0.139	0.416
05	0.285	0.064	0.196	0.456
06	0.201	0.053	0.434	0.311
07	0.151	0.148	0.34	0.361
08	0.011	0.352	0.233	0.404
09	0.0	0.872	0.005	0.123
10	0.0	0.909	0.0	0.091
11	0.151	0.0	0.0	0.849
12	0.0	0.0	0.0	1.0
13	0.0	0.0	0.0	1.0
14	0.0	0.0	1.0	0.0
15	0.0	0.0	0.0	1.0
16	0.005	0.19	0.002	0.802
17	0.171	0.616	0.036	0.178
18	0.136	0.264	0.196	0.404
19	0.226	0.253	0.174	0.347

PWM

	A	C	G	T
01	0.296	0.156	-0.75	0.014
02	0.079	0.279	-0.832	0.149
03	0.278	-0.116	-1.115	0.379
04	0.408	-1.278	-0.58	0.506
05	0.129	-1.33	-0.242	0.595
06	-0.215	-1.504	0.547	0.217
07	-0.495	-0.519	0.304	0.365
08	-2.931	0.34	-0.069	0.475
09	-4.497	1.241	-3.434	-0.7
10	-4.497	1.283	-4.497	-0.994
11	-0.495	-4.497	-4.497	1.214
12	-4.497	-4.497	-4.497	1.378
13	-4.497	-4.497	-4.497	1.378
14	-4.497	-4.497	1.378	-4.497
15	-4.497	-4.497	-4.497	1.378
16	-3.434	-0.269	-4.008	1.159
17	-0.376	0.895	-1.885	-0.336
18	-0.602	0.053	-0.239	0.477
19	-0.1	0.011	-0.355	0.325

Standard thresholds

P-value	Threshold
0.001	1.75276
0.0005	3.19876
0.0001	6.13156