HXA9.H12RSNP.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA9.H12RSNP.1.SM.D
Gene (human)	HOXA9 (GeneCards)
Gene synonyms (human)	HOX1G
Gene (mouse)	Hoxa9
Gene synonyms (mouse)	Hox-1.7, Hoxa-9
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	11
Consensus	nKTAATGRSvn
GC content	41.07%
Information content (bits; total / per base)	9.914 / 0.901
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8730

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 (24)	0.74	0.813	0.544	0.651	0.677	0.742	1.522	1.787	18.808	40.252
Mouse	5 (32)	0.598	0.771	0.425	0.596	0.494	0.67	1.019	1.558	16.305	68.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.929	0.883	0.912	0.863	0.883	0.833
Overall, 2 experiments	best	0.944	0.905	0.929	0.886	0.905	0.859
Methyl HT-SELEX, 1 experiments	median	0.944	0.905	0.929	0.886	0.905	0.859
Methyl HT-SELEX, 1 experiments	best	0.944	0.905	0.929	0.886	0.905	0.859
Non-Methyl HT-SELEX, 1 experiments	median	0.914	0.861	0.896	0.84	0.862	0.807
Non-Methyl HT-SELEX, 1 experiments	best	0.914	0.861	0.896	0.84	0.862	0.807

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	HOX9-13 {3.1.1.8} (TFClass)
TFClass ID	TFClass: 3.1.1.8.1
HGNC	HGNC:5109
MGI	MGI:96180
EntrezGene (human)	GeneID:3205 (SSTAR profile)
EntrezGene (mouse)	GeneID:15405 (SSTAR profile)
UniProt ID (human)	HXA9_HUMAN
UniProt ID (mouse)	HXA9_MOUSE
UniProt AC (human)	P31269 (TFClass)
UniProt AC (mouse)	P09631 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	4 human, 5 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	HXA9.H12RSNP.1.SM.D.pcm
PWM	HXA9.H12RSNP.1.SM.D.pwm
PFM	HXA9.H12RSNP.1.SM.D.pfm
Alignment	HXA9.H12RSNP.1.SM.D.words.tsv
Threshold to P-value map	HXA9.H12RSNP.1.SM.D.thr
Motif in other formats
JASPAR format	HXA9.H12RSNP.1.SM.D_jaspar_format.txt
MEME format	HXA9.H12RSNP.1.SM.D_meme_format.meme
Transfac format	HXA9.H12RSNP.1.SM.D_transfac_format.txt
Homer format	HXA9.H12RSNP.1.SM.D_homer_format_0.001.txt HXA9.H12RSNP.1.SM.D_homer_format_0.0005.txt HXA9.H12RSNP.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1907.25	2450.25	2865.25	1507.25
02	753.0	244.0	1763.0	5970.0
03	24.0	1.0	0.0	8705.0
04	6467.0	0.0	4.0	2259.0
05	8730.0	0.0	0.0	0.0
06	0.0	3681.0	0.0	5049.0
07	7.0	12.0	8306.0	405.0
08	5218.0	42.0	3028.0	442.0
09	202.0	4633.0	2035.0	1860.0
10	1448.0	3324.0	2610.0	1348.0
11	2180.5	2372.5	2072.5	2104.5

PFM

	A	C	G	T
01	0.218	0.281	0.328	0.173
02	0.086	0.028	0.202	0.684
03	0.003	0.0	0.0	0.997
04	0.741	0.0	0.0	0.259
05	1.0	0.0	0.0	0.0
06	0.0	0.422	0.0	0.578
07	0.001	0.001	0.951	0.046
08	0.598	0.005	0.347	0.051
09	0.023	0.531	0.233	0.213
10	0.166	0.381	0.299	0.154
11	0.25	0.272	0.237	0.241

PWM

	A	C	G	T
01	-0.135	0.116	0.272	-0.37
02	-1.062	-2.183	-0.213	1.006
03	-4.421	-6.505	-6.87	1.383
04	1.086	-6.87	-5.854	0.034
05	1.386	-6.87	-6.87	-6.87
06	-6.87	0.522	-6.87	0.838
07	-5.463	-5.031	1.336	-1.68
08	0.871	-3.899	0.327	-1.593
09	-2.37	0.752	-0.07	-0.16
10	-0.41	0.42	0.179	-0.481
11	-0.001	0.083	-0.052	-0.036

Standard thresholds

P-value	Threshold
0.001	5.069335
0.0005	6.08659
0.0001	7.6069