RUNX2.H12RSNP.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RUNX2.H12RSNP.0.P.B
Gene (human)	RUNX2 (GeneCards)
Gene synonyms (human)	AML3, CBFA1, OSF2, PEBP2A
Gene (mouse)	Runx2
Gene synonyms (mouse)	Aml3, Cbfa1, Osf2, Pebp2a
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	13
Consensus	nhTGYGGYbdvnn
GC content	54.24%
Information content (bits; total / per base)	9.289 / 0.715
Data sources	ChIP-Seq
Aligned words	984

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	4 (26)	0.903	0.941	0.795	0.883	0.888	0.918	3.164	3.549	159.516	287.796
Mouse	16 (101)	0.89	0.948	0.798	0.888	0.87	0.928	3.162	3.635	180.77	298.076

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.816	0.764	0.687	0.669	0.599	0.604
Overall, 3 experiments	best	0.97	0.949	0.913	0.89	0.782	0.779
Methyl HT-SELEX, 1 experiments	median	0.97	0.949	0.913	0.89	0.782	0.779
Methyl HT-SELEX, 1 experiments	best	0.97	0.949	0.913	0.89	0.782	0.779
Non-Methyl HT-SELEX, 2 experiments	median	0.768	0.719	0.656	0.638	0.583	0.586
Non-Methyl HT-SELEX, 2 experiments	best	0.816	0.764	0.687	0.669	0.599	0.604

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.606	5.591	0.258	0.176

TF superclass	Immunoglobulin fold {6} (TFClass)
TF class	Runt domain factors {6.4} (TFClass)
TF family	Runt-related {6.4.1} (TFClass)
TF subfamily	{6.4.1.0} (TFClass)
TFClass ID	TFClass: 6.4.1.0.1
HGNC	HGNC:10472
MGI	MGI:99829
EntrezGene (human)	GeneID:860 (SSTAR profile)
EntrezGene (mouse)	GeneID:12393 (SSTAR profile)
UniProt ID (human)	RUNX2_HUMAN
UniProt ID (mouse)	RUNX2_MOUSE
UniProt AC (human)	Q13950 (TFClass)
UniProt AC (mouse)	Q08775 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	4 human, 16 mouse
HT-SELEX	2
Methyl-HT-SELEX	1

PCM	RUNX2.H12RSNP.0.P.B.pcm
PWM	RUNX2.H12RSNP.0.P.B.pwm
PFM	RUNX2.H12RSNP.0.P.B.pfm
Alignment	RUNX2.H12RSNP.0.P.B.words.tsv
Threshold to P-value map	RUNX2.H12RSNP.0.P.B.thr
Motif in other formats
JASPAR format	RUNX2.H12RSNP.0.P.B_jaspar_format.txt
MEME format	RUNX2.H12RSNP.0.P.B_meme_format.meme
Transfac format	RUNX2.H12RSNP.0.P.B_transfac_format.txt
Homer format	RUNX2.H12RSNP.0.P.B_homer_format_0.001.txt RUNX2.H12RSNP.0.P.B_homer_format_0.0005.txt RUNX2.H12RSNP.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	127.0	299.0	264.0	294.0
02	87.0	526.0	73.0	298.0
03	62.0	14.0	29.0	879.0
04	10.0	17.0	930.0	27.0
05	66.0	206.0	33.0	679.0
06	16.0	0.0	940.0	28.0
07	5.0	22.0	946.0	11.0
08	22.0	110.0	106.0	746.0
09	74.0	303.0	91.0	516.0
10	359.0	61.0	158.0	406.0
11	176.0	281.0	371.0	156.0
12	184.0	273.0	285.0	242.0
13	177.0	237.0	364.0	206.0

PFM

	A	C	G	T
01	0.129	0.304	0.268	0.299
02	0.088	0.535	0.074	0.303
03	0.063	0.014	0.029	0.893
04	0.01	0.017	0.945	0.027
05	0.067	0.209	0.034	0.69
06	0.016	0.0	0.955	0.028
07	0.005	0.022	0.961	0.011
08	0.022	0.112	0.108	0.758
09	0.075	0.308	0.092	0.524
10	0.365	0.062	0.161	0.413
11	0.179	0.286	0.377	0.159
12	0.187	0.277	0.29	0.246
13	0.18	0.241	0.37	0.209

PWM

	A	C	G	T
01	-0.655	0.194	0.07	0.177
02	-1.027	0.756	-1.199	0.191
03	-1.358	-2.757	-2.087	1.268
04	-3.051	-2.583	1.325	-2.155
05	-1.297	-0.176	-1.965	1.011
06	-2.637	-4.968	1.335	-2.12
07	-3.607	-2.346	1.342	-2.969
08	-2.346	-0.796	-0.833	1.105
09	-1.185	0.207	-0.983	0.737
10	0.376	-1.374	-0.439	0.498
11	-0.332	0.132	0.409	-0.451
12	-0.288	0.103	0.146	-0.016
13	-0.326	-0.037	0.39	-0.176

Standard thresholds

P-value	Threshold
0.001	4.88946
0.0005	5.699765
0.0001	7.321515