SOX9.H12INVIVO.2.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SOX9.H12INVIVO.2.S.B
Gene (human)	SOX9 (GeneCards)
Gene synonyms (human)
Gene (mouse)	Sox9
Gene synonyms (mouse)	Sox-9
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	B

Motif length	17
Consensus	nvWvAATTdCAGTbAKn
GC content	33.04%
Information content (bits; total / per base)	16.8 / 0.988
Data sources	HT-SELEX
Aligned words	5809

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	1 (7)	0.454	0.477	0.298	0.319	0.347	0.569	0.701	1.361	0	0
Mouse	6 (41)	0.468	0.504	0.315	0.341	0.544	0.606	1.18	1.363	0	0.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Non-Methyl HT-SELEX, 4 experiments	median	0.656	0.65	0.588	0.586	0.553	0.554
Non-Methyl HT-SELEX, 4 experiments	best	0.72	0.705	0.631	0.623	0.581	0.579

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.608	0.222	0.579	0.384

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: 4.1.1.5.2
HGNC	HGNC:11204
MGI	MGI:98371
EntrezGene (human)	GeneID:6662 (SSTAR profile)
EntrezGene (mouse)	GeneID:20682 (SSTAR profile)
UniProt ID (human)	SOX9_HUMAN
UniProt ID (mouse)	SOX9_MOUSE
UniProt AC (human)	P48436 (TFClass)
UniProt AC (mouse)	Q04887 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 6 mouse
HT-SELEX	4
Methyl-HT-SELEX	0

PCM	SOX9.H12INVIVO.2.S.B.pcm
PWM	SOX9.H12INVIVO.2.S.B.pwm
PFM	SOX9.H12INVIVO.2.S.B.pfm
Alignment	SOX9.H12INVIVO.2.S.B.words.tsv
Threshold to P-value map	SOX9.H12INVIVO.2.S.B.thr
Motif in other formats
JASPAR format	SOX9.H12INVIVO.2.S.B_jaspar_format.txt
MEME format	SOX9.H12INVIVO.2.S.B_meme_format.meme
Transfac format	SOX9.H12INVIVO.2.S.B_transfac_format.txt
Homer format	SOX9.H12INVIVO.2.S.B_homer_format_0.001.txt SOX9.H12INVIVO.2.S.B_homer_format_0.0005.txt SOX9.H12INVIVO.2.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2117.0	1023.0	1236.0	1433.0
02	3507.0	883.0	743.0	676.0
03	1489.0	185.0	265.0	3870.0
04	1425.0	2112.0	2018.0	254.0
05	5613.0	33.0	21.0	142.0
06	5256.0	29.0	53.0	471.0
07	182.0	38.0	273.0	5316.0
08	23.0	29.0	753.0	5004.0
09	658.0	592.0	2604.0	1955.0
10	6.0	5138.0	8.0	657.0
11	5741.0	16.0	10.0	42.0
12	2.0	15.0	5591.0	201.0
13	7.0	20.0	20.0	5762.0
14	142.0	2301.0	2290.0	1076.0
15	4183.0	18.0	38.0	1570.0
16	327.75	840.75	928.75	3711.75
17	1810.75	941.75	1565.75	1490.75

PFM

	A	C	G	T
01	0.364	0.176	0.213	0.247
02	0.604	0.152	0.128	0.116
03	0.256	0.032	0.046	0.666
04	0.245	0.364	0.347	0.044
05	0.966	0.006	0.004	0.024
06	0.905	0.005	0.009	0.081
07	0.031	0.007	0.047	0.915
08	0.004	0.005	0.13	0.861
09	0.113	0.102	0.448	0.337
10	0.001	0.884	0.001	0.113
11	0.988	0.003	0.002	0.007
12	0.0	0.003	0.962	0.035
13	0.001	0.003	0.003	0.992
14	0.024	0.396	0.394	0.185
15	0.72	0.003	0.007	0.27
16	0.056	0.145	0.16	0.639
17	0.312	0.162	0.27	0.257

PWM

	A	C	G	T
01	0.376	-0.35	-0.161	-0.013
02	0.881	-0.497	-0.669	-0.763
03	0.025	-2.05	-1.694	0.979
04	-0.019	0.374	0.329	-1.737
05	1.351	-3.722	-4.14	-2.311
06	1.285	-3.843	-3.272	-1.123
07	-2.067	-3.589	-1.665	1.297
08	-4.057	-3.843	-0.655	1.236
09	-0.79	-0.895	0.583	0.297
10	-5.182	1.262	-4.963	-0.791
11	1.373	-4.383	-4.784	-3.494
12	-5.855	-4.439	1.347	-1.968
13	-5.067	-4.184	-4.184	1.377
14	-2.311	0.46	0.455	-0.299
15	1.057	-4.278	-3.589	0.078
16	-1.484	-0.545	-0.446	0.937
17	0.22	-0.432	0.075	0.026

Standard thresholds

P-value	Threshold
0.001	1.34821
0.0005	2.77391
0.0001	5.74266