HXA1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA1.H12INVIVO.0.SM.D
Gene (human)	HOXA1 (GeneCards)
Gene synonyms (human)	HOX1F
Gene (mouse)	Hoxa1
Gene synonyms (mouse)	Era-1, Hox-1.6, Hoxa-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	nnSbTAATKAbn
GC content	36.13%
Information content (bits; total / per base)	10.859 / 0.905
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9142

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.936	0.907	0.872	0.846	0.778	0.768
Overall, 4 experiments	best	0.979	0.967	0.964	0.945	0.935	0.91
Methyl HT-SELEX, 1 experiments	median	0.971	0.953	0.95	0.925	0.89	0.866
Methyl HT-SELEX, 1 experiments	best	0.971	0.953	0.95	0.925	0.89	0.866
Non-Methyl HT-SELEX, 3 experiments	median	0.902	0.861	0.794	0.766	0.667	0.671
Non-Methyl HT-SELEX, 3 experiments	best	0.979	0.967	0.964	0.945	0.935	0.91

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	HOX1 {3.1.1.1} (TFClass)
TFClass ID	TFClass: 3.1.1.1.1
HGNC	HGNC:5099
MGI	MGI:96170
EntrezGene (human)	GeneID:3198 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	HXA1_HUMAN
UniProt ID (mouse)	HXA1_MOUSE
UniProt AC (human)	P49639 (TFClass)
UniProt AC (mouse)	P09022 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	HXA1.H12INVIVO.0.SM.D.pcm
PWM	HXA1.H12INVIVO.0.SM.D.pwm
PFM	HXA1.H12INVIVO.0.SM.D.pfm
Alignment	HXA1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXA1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXA1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXA1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXA1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXA1.H12INVIVO.0.SM.D_homer_format_0.001.txt HXA1.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXA1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2020.25	1818.25	2455.25	2848.25
02	2000.5	3430.5	2352.5	1358.5
03	1520.0	2760.0	4655.0	207.0
04	183.0	3680.0	1954.0	3325.0
05	0.0	0.0	0.0	9142.0
06	9142.0	0.0	0.0	0.0
07	9142.0	0.0	0.0	0.0
08	0.0	220.0	0.0	8922.0
09	1.0	1017.0	2606.0	5518.0
10	7605.0	5.0	1522.0	10.0
11	1042.75	3315.75	2706.75	2076.75
12	1832.0	2742.0	2392.0	2176.0

PFM

	A	C	G	T
01	0.221	0.199	0.269	0.312
02	0.219	0.375	0.257	0.149
03	0.166	0.302	0.509	0.023
04	0.02	0.403	0.214	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	0.024	0.0	0.976
09	0.0	0.111	0.285	0.604
10	0.832	0.001	0.166	0.001
11	0.114	0.363	0.296	0.227
12	0.2	0.3	0.262	0.238

PWM

	A	C	G	T
01	-0.123	-0.228	0.072	0.22
02	-0.133	0.406	0.029	-0.52
03	-0.407	0.188	0.711	-2.392
04	-2.513	0.476	-0.157	0.375
05	-6.911	-6.911	-6.911	1.386
06	1.386	-6.911	-6.911	-6.911
07	1.386	-6.911	-6.911	-6.911
08	-6.911	-2.331	-6.911	1.361
09	-6.547	-0.808	0.131	0.881
10	1.202	-5.75	-0.406	-5.227
11	-0.784	0.372	0.169	-0.096
12	-0.221	0.182	0.046	-0.049

Standard thresholds

P-value	Threshold
0.001	4.310365
0.0005	5.909725
0.0001	7.820925