RUNX2.H12INVIVO.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RUNX2.H12INVIVO.1.S.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	1
Quality	B

Motif length	11
Consensus	nhTGCGGTYdn
GC content	50.44%
Information content (bits; total / per base)	12.002 / 1.091
Data sources	HT-SELEX
Aligned words	6833

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)	0.888	0.942	0.773	0.866	0.865	0.909	2.72	3.059	155.403	314.796
Mouse	16 (101)	0.885	0.929	0.781	0.857	0.854	0.903	2.674	3.121	176.699	331.252

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.859	0.828	0.722	0.71	0.624	0.632
Overall, 3 experiments	best	0.965	0.944	0.929	0.901	0.839	0.82
Methyl HT-SELEX, 1 experiments	median	0.965	0.944	0.929	0.901	0.839	0.82
Methyl HT-SELEX, 1 experiments	best	0.965	0.944	0.929	0.901	0.839	0.82
Non-Methyl HT-SELEX, 2 experiments	median	0.81	0.776	0.688	0.675	0.604	0.609
Non-Methyl HT-SELEX, 2 experiments	best	0.859	0.828	0.722	0.71	0.624	0.632

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	6.237	5.196	0.254	0.22

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.H12INVIVO.1.S.B.pcm
PWM	RUNX2.H12INVIVO.1.S.B.pwm
PFM	RUNX2.H12INVIVO.1.S.B.pfm
Alignment	RUNX2.H12INVIVO.1.S.B.words.tsv
Threshold to P-value map	RUNX2.H12INVIVO.1.S.B.thr
Motif in other formats
JASPAR format	RUNX2.H12INVIVO.1.S.B_jaspar_format.txt
MEME format	RUNX2.H12INVIVO.1.S.B_meme_format.meme
Transfac format	RUNX2.H12INVIVO.1.S.B_transfac_format.txt
Homer format	RUNX2.H12INVIVO.1.S.B_homer_format_0.001.txt RUNX2.H12INVIVO.1.S.B_homer_format_0.0005.txt RUNX2.H12INVIVO.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1593.0	1176.0	1525.0	2539.0
02	963.75	1025.75	872.75	3970.75
03	129.0	364.0	123.0	6217.0
04	1.0	0.0	6831.0	1.0
05	13.0	5605.0	0.0	1215.0
06	0.0	0.0	6833.0	0.0
07	0.0	0.0	6833.0	0.0
08	5.0	0.0	49.0	6779.0
09	473.0	909.0	628.0	4823.0
10	2632.5	488.5	1213.5	2498.5
11	1541.5	1378.5	2056.5	1856.5

PFM

	A	C	G	T
01	0.233	0.172	0.223	0.372
02	0.141	0.15	0.128	0.581
03	0.019	0.053	0.018	0.91
04	0.0	0.0	1.0	0.0
05	0.002	0.82	0.0	0.178
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	0.001	0.0	0.007	0.992
09	0.069	0.133	0.092	0.706
10	0.385	0.071	0.178	0.366
11	0.226	0.202	0.301	0.272

PWM

	A	C	G	T
01	-0.07	-0.373	-0.113	0.396
02	-0.571	-0.509	-0.67	0.843
03	-2.568	-1.541	-2.615	1.291
04	-6.279	-6.653	1.385	-6.279
05	-4.723	1.187	-6.653	-0.34
06	-6.653	-6.653	1.385	-6.653
07	-6.653	-6.653	1.385	-6.653
08	-5.469	-6.653	-3.509	1.377
09	-1.281	-0.63	-0.998	1.037
10	0.432	-1.249	-0.341	0.38
11	-0.103	-0.214	0.185	0.083

Standard thresholds

P-value	Threshold
0.001	3.51197
0.0005	5.094195
0.0001	7.560965