HXA9.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA9.H12INVITRO.0.P.B
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	0
Quality	B

Motif length	12
Consensus	dWRATTKATKdb
GC content	31.13%
Information content (bits; total / per base)	10.77 / 0.897
Data sources	ChIP-Seq
Aligned words	1000

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)	0.764	0.85	0.561	0.772	0.776	0.85	2.111	3.203	14.232	242.62
Mouse	5 (32)	0.755	0.904	0.64	0.843	0.72	0.888	2.194	3.533	109.431	233.921

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.786	0.712	0.748	0.682	0.702	0.65
Overall, 2 experiments	best	0.804	0.73	0.766	0.699	0.718	0.665
Methyl HT-SELEX, 1 experiments	median	0.804	0.73	0.766	0.699	0.718	0.665
Methyl HT-SELEX, 1 experiments	best	0.804	0.73	0.766	0.699	0.718	0.665
Non-Methyl HT-SELEX, 1 experiments	median	0.768	0.695	0.73	0.666	0.686	0.636
Non-Methyl HT-SELEX, 1 experiments	best	0.768	0.695	0.73	0.666	0.686	0.636

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.H12INVITRO.0.P.B.pcm
PWM	HXA9.H12INVITRO.0.P.B.pwm
PFM	HXA9.H12INVITRO.0.P.B.pfm
Alignment	HXA9.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	HXA9.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	HXA9.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	HXA9.H12INVITRO.0.P.B_meme_format.meme
Transfac format	HXA9.H12INVITRO.0.P.B_transfac_format.txt
Homer format	HXA9.H12INVITRO.0.P.B_homer_format_0.001.txt HXA9.H12INVITRO.0.P.B_homer_format_0.0005.txt HXA9.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	404.0	132.0	273.0	191.0
02	221.0	18.0	79.0	682.0
03	150.0	17.0	771.0	62.0
04	827.0	25.0	18.0	130.0
05	28.0	15.0	49.0	908.0
06	26.0	10.0	48.0	916.0
07	79.0	80.0	169.0	672.0
08	973.0	14.0	13.0	0.0
09	10.0	112.0	21.0	857.0
10	145.0	8.0	572.0	275.0
11	296.0	49.0	512.0	143.0
12	76.0	522.0	209.0	193.0

PFM

	A	C	G	T
01	0.404	0.132	0.273	0.191
02	0.221	0.018	0.079	0.682
03	0.15	0.017	0.771	0.062
04	0.827	0.025	0.018	0.13
05	0.028	0.015	0.049	0.908
06	0.026	0.01	0.048	0.916
07	0.079	0.08	0.169	0.672
08	0.973	0.014	0.013	0.0
09	0.01	0.112	0.021	0.857
10	0.145	0.008	0.572	0.275
11	0.296	0.049	0.512	0.143
12	0.076	0.522	0.209	0.193

PWM

	A	C	G	T
01	0.477	-0.633	0.087	-0.267
02	-0.122	-2.546	-1.137	0.999
03	-0.506	-2.598	1.122	-1.374
04	1.192	-2.243	-2.546	-0.648
05	-2.136	-2.711	-1.602	1.285
06	-2.206	-3.066	-1.622	1.294
07	-1.137	-1.125	-0.388	0.984
08	1.354	-2.773	-2.839	-4.982
09	-3.066	-0.795	-2.405	1.227
10	-0.54	-3.253	0.824	0.095
11	0.168	-1.602	0.713	-0.553
12	-1.175	0.733	-0.178	-0.257

Standard thresholds

P-value	Threshold
0.001	4.54731
0.0005	5.428115
0.0001	7.246135