HXA9.H12CORE.2.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA9.H12CORE.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	10
Consensus	YTTTATKRSn
GC content	29.24%
Information content (bits; total / per base)	11.466 / 1.147
Data sources	ChIP-Seq
Aligned words	998

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)	0.778	0.833	0.624	0.71	0.819	0.872	2.434	2.889	25.209	58.553
Mouse	5 (32)	0.55	0.76	0.392	0.626	0.519	0.746	1.172	2.156	16.659	73.036

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.883	0.825	0.848	0.789	0.797	0.744
Overall, 2 experiments	best	0.9	0.847	0.868	0.811	0.817	0.765
Methyl HT-SELEX, 1 experiments	median	0.9	0.847	0.868	0.811	0.817	0.765
Methyl HT-SELEX, 1 experiments	best	0.9	0.847	0.868	0.811	0.817	0.765
Non-Methyl HT-SELEX, 1 experiments	median	0.866	0.804	0.829	0.767	0.777	0.723
Non-Methyl HT-SELEX, 1 experiments	best	0.866	0.804	0.829	0.767	0.777	0.723

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.H12CORE.2.P.B.pcm
PWM	HXA9.H12CORE.2.P.B.pwm
PFM	HXA9.H12CORE.2.P.B.pfm
Alignment	HXA9.H12CORE.2.P.B.words.tsv
Threshold to P-value map	HXA9.H12CORE.2.P.B.thr
Motif in other formats
JASPAR format	HXA9.H12CORE.2.P.B_jaspar_format.txt
MEME format	HXA9.H12CORE.2.P.B_meme_format.meme
Transfac format	HXA9.H12CORE.2.P.B_transfac_format.txt
Homer format	HXA9.H12CORE.2.P.B_homer_format_0.001.txt HXA9.H12CORE.2.P.B_homer_format_0.0005.txt HXA9.H12CORE.2.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	75.0	115.0	71.0	737.0
02	6.0	7.0	22.0	963.0
03	8.0	15.0	4.0	971.0
04	72.0	25.0	28.0	873.0
05	982.0	7.0	7.0	2.0
06	12.0	51.0	31.0	904.0
07	92.0	5.0	466.0	435.0
08	167.0	16.0	736.0	79.0
09	30.0	724.0	182.0	62.0
10	209.0	383.0	23.0	383.0

PFM

	A	C	G	T
01	0.075	0.115	0.071	0.738
02	0.006	0.007	0.022	0.965
03	0.008	0.015	0.004	0.973
04	0.072	0.025	0.028	0.875
05	0.984	0.007	0.007	0.002
06	0.012	0.051	0.031	0.906
07	0.092	0.005	0.467	0.436
08	0.167	0.016	0.737	0.079
09	0.03	0.725	0.182	0.062
10	0.209	0.384	0.023	0.384

PWM

	A	C	G	T
01	-1.186	-0.767	-1.24	1.079
02	-3.482	-3.36	-2.36	1.345
03	-3.252	-2.709	-3.781	1.354
04	-1.226	-2.241	-2.134	1.248
05	1.365	-3.36	-3.36	-4.211
06	-2.907	-1.561	-2.038	1.282
07	-0.986	-3.62	0.622	0.553
08	-0.398	-2.651	1.077	-1.135
09	-2.069	1.061	-0.313	-1.372
10	-0.176	0.426	-2.318	0.426

Standard thresholds

P-value	Threshold
0.001	4.29423
0.0005	5.28398
0.0001	7.21563