RUNX2.H12RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	RUNX2.H12RSNP.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	nWTGCGGTYdn
GC content	49.66%
Information content (bits; total / per base)	13.305 / 1.21
Data sources	HT-SELEX
Aligned words	599

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)	0.846	0.917	0.738	0.844	0.83	0.883	2.377	2.804	119.93	285.921
Mouse	16 (101)	0.861	0.903	0.762	0.832	0.826	0.877	2.398	2.822	153.076	298.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 3 experiments	median	0.854	0.821	0.716	0.705	0.619	0.628
Overall, 3 experiments	best	0.947	0.916	0.918	0.879	0.832	0.807
Methyl HT-SELEX, 1 experiments	median	0.947	0.916	0.918	0.879	0.832	0.807
Methyl HT-SELEX, 1 experiments	best	0.947	0.916	0.918	0.879	0.832	0.807
Non-Methyl HT-SELEX, 2 experiments	median	0.806	0.771	0.681	0.67	0.6	0.606
Non-Methyl HT-SELEX, 2 experiments	best	0.854	0.821	0.716	0.705	0.619	0.628

rSNP benchmarking, ADASTRA	odds-ratio	-log-Fisher's P	Pearson r	Kendall tau
#	7.295	5.302	0.254	0.228

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.1.S.B.pcm
PWM	RUNX2.H12RSNP.1.S.B.pwm
PFM	RUNX2.H12RSNP.1.S.B.pfm
Alignment	RUNX2.H12RSNP.1.S.B.words.tsv
Threshold to P-value map	RUNX2.H12RSNP.1.S.B.thr
Motif in other formats
JASPAR format	RUNX2.H12RSNP.1.S.B_jaspar_format.txt
MEME format	RUNX2.H12RSNP.1.S.B_meme_format.meme
Transfac format	RUNX2.H12RSNP.1.S.B_transfac_format.txt
Homer format	RUNX2.H12RSNP.1.S.B_homer_format_0.001.txt RUNX2.H12RSNP.1.S.B_homer_format_0.0005.txt RUNX2.H12RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	160.75	142.75	101.75	193.75
02	70.0	63.0	64.0	402.0
03	0.0	16.0	0.0	583.0
04	0.0	0.0	599.0	0.0
05	0.0	571.0	0.0	28.0
06	0.0	0.0	599.0	0.0
07	0.0	0.0	599.0	0.0
08	0.0	0.0	0.0	599.0
09	33.0	56.0	41.0	469.0
10	239.25	48.25	89.25	222.25
11	153.5	128.5	153.5	163.5

PFM

	A	C	G	T
01	0.268	0.238	0.17	0.323
02	0.117	0.105	0.107	0.671
03	0.0	0.027	0.0	0.973
04	0.0	0.0	1.0	0.0
05	0.0	0.953	0.0	0.047
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.055	0.093	0.068	0.783
10	0.399	0.081	0.149	0.371
11	0.256	0.215	0.256	0.273

PWM

	A	C	G	T
01	0.07	-0.047	-0.381	0.255
02	-0.749	-0.851	-0.836	0.981
03	-4.55	-2.152	-4.55	1.351
04	-4.55	-4.55	1.378	-4.55
05	-4.55	1.331	-4.55	-1.632
06	-4.55	-4.55	1.378	-4.55
07	-4.55	-4.55	1.378	-4.55
08	-4.55	-4.55	-4.55	1.378
09	-1.476	-0.966	-1.268	1.134
10	0.465	-1.111	-0.51	0.391
11	0.024	-0.151	0.024	0.087

Standard thresholds

P-value	Threshold
0.001	3.023975
0.0005	4.451045
0.0001	7.272075