HXC13.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC13.H12INVIVO.0.SM.D
Gene (human)	HOXC13 (GeneCards)
Gene synonyms (human)	HOX3G
Gene (mouse)	Hoxc13
Gene synonyms (mouse)	Hoxc-13
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	ndTTTACGAGvn
GC content	41.06%
Information content (bits; total / per base)	14.115 / 1.176
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9145

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.991	0.987	0.915	0.917	0.818	0.831
Overall, 4 experiments	best	0.999	0.998	0.997	0.996	0.985	0.981
Methyl HT-SELEX, 1 experiments	median	0.999	0.998	0.997	0.996	0.985	0.981
Methyl HT-SELEX, 1 experiments	best	0.999	0.998	0.997	0.996	0.985	0.981
Non-Methyl HT-SELEX, 3 experiments	median	0.984	0.977	0.838	0.845	0.675	0.71
Non-Methyl HT-SELEX, 3 experiments	best	0.998	0.996	0.992	0.989	0.961	0.953

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: 3.1.1.8.16
HGNC	HGNC:5125
MGI	MGI:99560
EntrezGene (human)	GeneID:3229 (SSTAR profile)
EntrezGene (mouse)	GeneID:15422 (SSTAR profile)
UniProt ID (human)	HXC13_HUMAN
UniProt ID (mouse)	HXC13_MOUSE
UniProt AC (human)	P31276 (TFClass)
UniProt AC (mouse)	P50207 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXC13.H12INVIVO.0.SM.D.pcm
PWM	HXC13.H12INVIVO.0.SM.D.pwm
PFM	HXC13.H12INVIVO.0.SM.D.pfm
Alignment	HXC13.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXC13.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXC13.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXC13.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXC13.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXC13.H12INVIVO.0.SM.D_homer_format_0.001.txt HXC13.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXC13.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2155.75	1841.75	3223.75	1923.75
02	1567.5	874.5	2058.5	4644.5
03	180.0	39.0	187.0	8739.0
04	93.0	4.0	2.0	9046.0
05	650.0	5.0	2.0	8488.0
06	9143.0	1.0	0.0	1.0
07	0.0	8035.0	1.0	1109.0
08	69.0	1.0	9027.0	48.0
09	8966.0	27.0	120.0	32.0
10	37.0	678.0	7905.0	525.0
11	1569.5	3508.5	2948.5	1118.5
12	1839.75	2176.75	2390.75	2737.75

PFM

	A	C	G	T
01	0.236	0.201	0.353	0.21
02	0.171	0.096	0.225	0.508
03	0.02	0.004	0.02	0.956
04	0.01	0.0	0.0	0.989
05	0.071	0.001	0.0	0.928
06	1.0	0.0	0.0	0.0
07	0.0	0.879	0.0	0.121
08	0.008	0.0	0.987	0.005
09	0.98	0.003	0.013	0.003
10	0.004	0.074	0.864	0.057
11	0.172	0.384	0.322	0.122
12	0.201	0.238	0.261	0.299

PWM

	A	C	G	T
01	-0.059	-0.216	0.343	-0.172
02	-0.377	-0.959	-0.105	0.708
03	-2.53	-4.015	-2.492	1.34
04	-3.179	-5.898	-6.282	1.375
05	-1.255	-5.751	-6.282	1.311
06	1.385	-6.548	-6.911	-6.548
07	-6.911	1.256	-6.548	-0.722
08	-3.469	-6.548	1.373	-3.818
09	1.366	-4.359	-2.929	-4.201
10	-4.065	-1.213	1.24	-1.468
11	-0.376	0.428	0.254	-0.714
12	-0.217	-0.049	0.045	0.18

Standard thresholds

P-value	Threshold
0.001	2.23387
0.0005	3.655845
0.0001	6.66831