HXA5.H12INVITRO.0.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA5.H12INVITRO.0.SM.B
Gene (human)	HOXA5 (GeneCards)
Gene synonyms (human)	HOX1C
Gene (mouse)	Hoxa5
Gene synonyms (mouse)	Hox-1.3, Hoxa-5
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	12
Consensus	nnvbTAATKRbn
GC content	37.44%
Information content (bits; total / per base)	10.382 / 0.865
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9703

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.956	0.932	0.927	0.894	0.864	0.832
Overall, 4 experiments	best	0.966	0.946	0.94	0.912	0.883	0.854
Methyl HT-SELEX, 2 experiments	median	0.959	0.936	0.925	0.894	0.848	0.823
Methyl HT-SELEX, 2 experiments	best	0.966	0.946	0.94	0.912	0.883	0.854
Non-Methyl HT-SELEX, 2 experiments	median	0.956	0.932	0.927	0.894	0.864	0.832
Non-Methyl HT-SELEX, 2 experiments	best	0.959	0.935	0.932	0.9	0.875	0.843

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	HOX5 {3.1.1.5} (TFClass)
TFClass ID	TFClass: 3.1.1.5.1
HGNC	HGNC:5106
MGI	MGI:96177
EntrezGene (human)	GeneID:3202 (SSTAR profile)
EntrezGene (mouse)	GeneID:15402 (SSTAR profile)
UniProt ID (human)	HXA5_HUMAN
UniProt ID (mouse)	HXA5_MOUSE
UniProt AC (human)	P20719 (TFClass)
UniProt AC (mouse)	P09021 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	2
Methyl-HT-SELEX	2

PCM	HXA5.H12INVITRO.0.SM.B.pcm
PWM	HXA5.H12INVITRO.0.SM.B.pwm
PFM	HXA5.H12INVITRO.0.SM.B.pfm
Alignment	HXA5.H12INVITRO.0.SM.B.words.tsv
Threshold to P-value map	HXA5.H12INVITRO.0.SM.B.thr
Motif in other formats
JASPAR format	HXA5.H12INVITRO.0.SM.B_jaspar_format.txt
MEME format	HXA5.H12INVITRO.0.SM.B_meme_format.meme
Transfac format	HXA5.H12INVITRO.0.SM.B_transfac_format.txt
Homer format	HXA5.H12INVITRO.0.SM.B_homer_format_0.001.txt HXA5.H12INVITRO.0.SM.B_homer_format_0.0005.txt HXA5.H12INVITRO.0.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	3005.25	1930.25	2337.25	2430.25
02	1915.5	3818.5	1949.5	2019.5
03	2103.0	3117.0	4118.0	365.0
04	426.0	3891.0	1852.0	3534.0
05	0.0	1.0	2.0	9700.0
06	9703.0	0.0	0.0	0.0
07	9703.0	0.0	0.0	0.0
08	0.0	42.0	0.0	9661.0
09	23.0	303.0	4778.0	4599.0
10	6016.0	242.0	3072.0	373.0
11	972.5	4579.5	2228.5	1922.5
12	2113.25	2818.25	2513.25	2258.25

PFM

	A	C	G	T
01	0.31	0.199	0.241	0.25
02	0.197	0.394	0.201	0.208
03	0.217	0.321	0.424	0.038
04	0.044	0.401	0.191	0.364
05	0.0	0.0	0.0	1.0
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.004	0.0	0.996
09	0.002	0.031	0.492	0.474
10	0.62	0.025	0.317	0.038
11	0.1	0.472	0.23	0.198
12	0.218	0.29	0.259	0.233

PWM

	A	C	G	T
01	0.214	-0.228	-0.037	0.002
02	-0.236	0.453	-0.218	-0.183
03	-0.143	0.251	0.529	-1.889
04	-1.735	0.472	-0.27	0.376
05	-6.964	-6.602	-6.337	1.385
06	1.386	-6.964	-6.964	-6.964
07	1.386	-6.964	-6.964	-6.964
08	-6.964	-4.004	-6.964	1.381
09	-4.564	-2.074	0.677	0.639
10	0.908	-2.296	0.236	-1.867
11	-0.913	0.635	-0.085	-0.232
12	-0.138	0.15	0.035	-0.071

Standard thresholds

P-value	Threshold
0.001	4.76111
0.0005	6.099665
0.0001	7.745095