HXD9.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD9.H12INVIVO.0.SM.D
Gene (human)	HOXD9 (GeneCards)
Gene synonyms (human)	HOX4C
Gene (mouse)	Hoxd9
Gene synonyms (mouse)	Hox-4.4, Hoxd-9
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	13
Consensus	nnWTTTACGAYbn
GC content	38.79%
Information content (bits; total / per base)	14.105 / 1.085
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	2002

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.992	0.986	0.979	0.969	0.954	0.938
Overall, 4 experiments	best	0.995	0.993	0.988	0.982	0.963	0.952
Methyl HT-SELEX, 2 experiments	median	0.992	0.986	0.979	0.97	0.943	0.929
Methyl HT-SELEX, 2 experiments	best	0.995	0.991	0.988	0.982	0.963	0.952
Non-Methyl HT-SELEX, 2 experiments	median	0.991	0.986	0.979	0.969	0.954	0.938
Non-Methyl HT-SELEX, 2 experiments	best	0.995	0.993	0.986	0.98	0.962	0.95

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: 3.1.1.8.4
HGNC	HGNC:5140
MGI	MGI:96210
EntrezGene (human)	GeneID:3235 (SSTAR profile)
EntrezGene (mouse)	GeneID:15438 (SSTAR profile)
UniProt ID (human)	HXD9_HUMAN
UniProt ID (mouse)	HXD9_MOUSE
UniProt AC (human)	P28356 (TFClass)
UniProt AC (mouse)	P28357 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXD9.H12INVIVO.0.SM.D.pcm
PWM	HXD9.H12INVIVO.0.SM.D.pwm
PFM	HXD9.H12INVIVO.0.SM.D.pfm
Alignment	HXD9.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	HXD9.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	HXD9.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	HXD9.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	HXD9.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	HXD9.H12INVIVO.0.SM.D_homer_format_0.001.txt HXD9.H12INVIVO.0.SM.D_homer_format_0.0005.txt HXD9.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	615.75	601.75	403.75	380.75
02	513.0	457.0	663.0	369.0
03	278.0	163.0	218.0	1343.0
04	19.0	1.0	3.0	1979.0
05	0.0	0.0	0.0	2002.0
06	272.0	0.0	0.0	1730.0
07	2002.0	0.0	0.0	0.0
08	0.0	1504.0	0.0	498.0
09	0.0	0.0	1981.0	21.0
10	1903.0	0.0	98.0	1.0
11	0.0	1507.0	216.0	279.0
12	229.75	1140.75	294.75	336.75
13	490.75	449.75	394.75	666.75

PFM

	A	C	G	T
01	0.308	0.301	0.202	0.19
02	0.256	0.228	0.331	0.184
03	0.139	0.081	0.109	0.671
04	0.009	0.0	0.001	0.989
05	0.0	0.0	0.0	1.0
06	0.136	0.0	0.0	0.864
07	1.0	0.0	0.0	0.0
08	0.0	0.751	0.0	0.249
09	0.0	0.0	0.99	0.01
10	0.951	0.0	0.049	0.0
11	0.0	0.753	0.108	0.139
12	0.115	0.57	0.147	0.168
13	0.245	0.225	0.197	0.333

PWM

	A	C	G	T
01	0.207	0.184	-0.214	-0.272
02	0.025	-0.091	0.28	-0.303
03	-0.585	-1.114	-0.826	0.985
04	-3.18	-5.155	-4.63	1.372
05	-5.577	-5.577	-5.577	1.383
06	-0.607	-5.577	-5.577	1.238
07	1.383	-5.577	-5.577	-5.577
08	-5.577	1.098	-5.577	-0.005
09	-5.577	-5.577	1.373	-3.088
10	1.333	-5.577	-1.615	-5.155
11	-5.577	1.1	-0.835	-0.581
12	-0.774	0.822	-0.527	-0.394
13	-0.02	-0.106	-0.236	0.286

Standard thresholds

P-value	Threshold
0.001	2.10401
0.0005	3.50796
0.0001	6.96879