HXD1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD1.H12INVIVO.0.SM.D
Gene (human)	HOXD1 (GeneCards)
Gene synonyms (human)	HOX4, HOX4G
Gene (mouse)	Hoxd1
Gene synonyms (mouse)	Hox-4.9, Hoxd-1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nvvYTAATTASvn
GC content	33.93%
Information content (bits; total / per base)	13.084 / 1.006
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2447

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.927	0.895	0.849	0.819	0.745	0.734
Overall, 2 experiments	best	0.949	0.919	0.908	0.872	0.821	0.795
Methyl HT-SELEX, 1 experiments	median	0.906	0.872	0.789	0.766	0.668	0.673
Methyl HT-SELEX, 1 experiments	best	0.906	0.872	0.789	0.766	0.668	0.673
Non-Methyl HT-SELEX, 1 experiments	median	0.949	0.919	0.908	0.872	0.821	0.795
Non-Methyl HT-SELEX, 1 experiments	best	0.949	0.919	0.908	0.872	0.821	0.795

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: 3.1.1.1.3
HGNC	HGNC:5132
MGI	MGI:96201
EntrezGene (human)	GeneID:3231 (SSTAR profile)
EntrezGene (mouse)	GeneID:15429 (SSTAR profile)
UniProt ID (human)	HXD1_HUMAN
UniProt ID (mouse)	HXD1_MOUSE
UniProt AC (human)	Q9GZZ0 (TFClass)
UniProt AC (mouse)	Q01822 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXD1.H12INVIVO.0.SM.D.pcm
PWM	HXD1.H12INVIVO.0.SM.D.pwm
PFM	HXD1.H12INVIVO.0.SM.D.pfm
Alignment	HXD1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXD1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXD1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXD1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXD1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXD1.H12INVIVO.0.SM.D_homer_format_0.001.txt HXD1.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXD1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	639.0	519.0	549.0	740.0
02	652.75	902.75	649.75	241.75
03	931.0	614.0	892.0	10.0
04	3.0	1080.0	385.0	979.0
05	1.0	45.0	0.0	2401.0
06	2442.0	0.0	5.0	0.0
07	2447.0	0.0	0.0	0.0
08	0.0	0.0	0.0	2447.0
09	0.0	16.0	25.0	2406.0
10	2232.0	0.0	213.0	2.0
11	92.0	1408.0	815.0	132.0
12	459.5	977.5	660.5	349.5
13	567.25	607.25	430.25	842.25

PFM

	A	C	G	T
01	0.261	0.212	0.224	0.302
02	0.267	0.369	0.266	0.099
03	0.38	0.251	0.365	0.004
04	0.001	0.441	0.157	0.4
05	0.0	0.018	0.0	0.981
06	0.998	0.0	0.002	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.007	0.01	0.983
10	0.912	0.0	0.087	0.001
11	0.038	0.575	0.333	0.054
12	0.188	0.399	0.27	0.143
13	0.232	0.248	0.176	0.344

PWM

	A	C	G	T
01	0.043	-0.164	-0.108	0.19
02	0.065	0.388	0.06	-0.924
03	0.419	0.004	0.376	-3.939
04	-4.82	0.567	-0.461	0.469
05	-5.337	-2.57	-5.751	1.365
06	1.382	-5.751	-4.481	-5.751
07	1.384	-5.751	-5.751	-5.751
08	-5.751	-5.751	-5.751	1.384
09	-5.751	-3.532	-3.125	1.367
10	1.292	-5.751	-1.049	-5.046
11	-1.877	0.832	0.286	-1.522
12	-0.285	0.467	0.076	-0.557
13	-0.075	-0.007	-0.351	0.319

Standard thresholds

P-value	Threshold
0.001	2.55201
0.0005	3.794415
0.0001	7.310975