HXA9.H12INVIVO.2.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA9.H12INVIVO.2.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	2
Quality	B

Motif length	12
Consensus	dnTTWATKRYYd
GC content	32.71%
Information content (bits; total / per base)	10.331 / 0.861
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)	0.733	0.808	0.575	0.653	0.794	0.847	2.306	2.668	25.325	82.086
Mouse	5 (32)	0.597	0.793	0.443	0.68	0.59	0.788	1.459	2.523	31.211	108.201

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.855	0.792	0.807	0.748	0.749	0.701
Overall, 2 experiments	best	0.87	0.81	0.825	0.766	0.768	0.718
Methyl HT-SELEX, 1 experiments	median	0.87	0.81	0.825	0.766	0.768	0.718
Methyl HT-SELEX, 1 experiments	best	0.87	0.81	0.825	0.766	0.768	0.718
Non-Methyl HT-SELEX, 1 experiments	median	0.839	0.774	0.79	0.729	0.73	0.683
Non-Methyl HT-SELEX, 1 experiments	best	0.839	0.774	0.79	0.729	0.73	0.683

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.H12INVIVO.2.P.B.pcm
PWM	HXA9.H12INVIVO.2.P.B.pwm
PFM	HXA9.H12INVIVO.2.P.B.pfm
Alignment	HXA9.H12INVIVO.2.P.B.words.tsv
Threshold to P-value map	HXA9.H12INVIVO.2.P.B.thr
Motif in other formats
JASPAR format	HXA9.H12INVIVO.2.P.B_jaspar_format.txt
MEME format	HXA9.H12INVIVO.2.P.B_meme_format.meme
Transfac format	HXA9.H12INVIVO.2.P.B_transfac_format.txt
Homer format	HXA9.H12INVIVO.2.P.B_homer_format_0.001.txt HXA9.H12INVIVO.2.P.B_homer_format_0.0005.txt HXA9.H12INVIVO.2.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	296.0	130.0	357.0	217.0
02	358.0	118.0	118.0	406.0
03	4.0	12.0	7.0	977.0
04	15.0	20.0	18.0	947.0
05	88.0	52.0	57.0	803.0
06	819.0	20.0	159.0	2.0
07	2.0	30.0	9.0	959.0
08	75.0	2.0	678.0	245.0
09	195.0	15.0	696.0	94.0
10	20.0	547.0	142.0	291.0
11	106.0	327.0	42.0	525.0
12	176.0	127.0	242.0	455.0

PFM

	A	C	G	T
01	0.296	0.13	0.357	0.217
02	0.358	0.118	0.118	0.406
03	0.004	0.012	0.007	0.977
04	0.015	0.02	0.018	0.947
05	0.088	0.052	0.057	0.803
06	0.819	0.02	0.159	0.002
07	0.002	0.03	0.009	0.959
08	0.075	0.002	0.678	0.245
09	0.195	0.015	0.696	0.094
10	0.02	0.547	0.142	0.291
11	0.106	0.327	0.042	0.525
12	0.176	0.127	0.242	0.455

PWM

	A	C	G	T
01	0.168	-0.648	0.354	-0.141
02	0.357	-0.743	-0.743	0.482
03	-3.783	-2.909	-3.362	1.358
04	-2.711	-2.45	-2.546	1.327
05	-1.032	-1.544	-1.455	1.162
06	1.182	-2.45	-0.449	-4.213
07	-4.213	-2.071	-3.156	1.339
08	-1.188	-4.213	0.993	-0.02
09	-0.247	-2.711	1.019	-0.967
10	-2.45	0.779	-0.56	0.151
11	-0.849	0.267	-1.75	0.738
12	-0.348	-0.671	-0.032	0.596

Standard thresholds

P-value	Threshold
0.001	4.67657
0.0005	5.569715
0.0001	7.35993