HXC10.H14RSNP.2.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC10.H14RSNP.2.SM.D
Gene (human)	HOXC10 (GeneCards)
Gene synonyms (human)	HOX3I
Gene (mouse)	Hoxc10
Gene synonyms (mouse)	Hox-3.6, Hoxc-10
LOGO
LOGO (reverse complement)
Motif subtype	2
Quality	D

Motif length	12
Consensus	ndTTTACGAYbn
GC content	37.55%
Information content (bits; total / per base)	13.674 / 1.139
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8893
Previous names	HXC10.H12RSNP.2.SM.D

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Mouse	2 (10)	0.629	0.677	0.475	0.531	0.619	0.673	1.554	1.776	15.182	26.538

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.959	0.942	0.912	0.886	0.826	0.806
Overall, 8 experiments	best	0.999	0.998	0.997	0.996	0.981	0.977
Methyl HT-SELEX, 2 experiments	median	0.998	0.996	0.995	0.992	0.969	0.964
Methyl HT-SELEX, 2 experiments	best	0.999	0.998	0.997	0.996	0.981	0.977
Non-Methyl HT-SELEX, 6 experiments	median	0.895	0.857	0.833	0.791	0.742	0.717
Non-Methyl HT-SELEX, 6 experiments	best	0.996	0.994	0.989	0.984	0.956	0.946

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: 3.1.1.8.7
HGNC	HGNC:5122
MGI	MGI:96192
EntrezGene (human)	GeneID:3226 (SSTAR profile)
EntrezGene (mouse)	GeneID:209448 (SSTAR profile)
UniProt ID (human)	HXC10_HUMAN
UniProt ID (mouse)	HXC10_MOUSE
UniProt AC (human)	Q9NYD6 (TFClass)
UniProt AC (mouse)	P31257 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 2 mouse
HT-SELEX	6
Methyl-HT-SELEX	2
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	HXC10.H14RSNP.2.SM.D.pcm
PWM	HXC10.H14RSNP.2.SM.D.pwm
PFM	HXC10.H14RSNP.2.SM.D.pfm
Threshold to P-value map	HXC10.H14RSNP.2.SM.D.thr
Motif in other formats
JASPAR format	HXC10.H14RSNP.2.SM.D_jaspar_format.txt
MEME format	HXC10.H14RSNP.2.SM.D_meme_format.meme
Transfac format	HXC10.H14RSNP.2.SM.D_transfac_format.txt
Homer format	HXC10.H14RSNP.2.SM.D_homer_format_0.001.txt HXC10.H14RSNP.2.SM.D_homer_format_0.0005.txt HXC10.H14RSNP.2.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2318.75	1998.75	2851.75	1723.75
02	1543.25	832.25	1209.25	5308.25
03	268.0	29.0	131.0	8465.0
04	12.0	6.0	4.0	8871.0
05	857.0	0.0	0.0	8036.0
06	8890.0	0.0	0.0	3.0
07	1.0	7526.0	0.0	1366.0
08	1.0	4.0	8633.0	255.0
09	8703.0	11.0	149.0	30.0
10	13.0	5664.0	959.0	2257.0
11	1068.0	4599.0	1908.0	1318.0
12	1821.0	1902.0	1660.0	3510.0

PFM

	A	C	G	T
01	0.261	0.225	0.321	0.194
02	0.174	0.094	0.136	0.597
03	0.03	0.003	0.015	0.952
04	0.001	0.001	0.0	0.998
05	0.096	0.0	0.0	0.904
06	1.0	0.0	0.0	0.0
07	0.0	0.846	0.0	0.154
08	0.0	0.0	0.971	0.029
09	0.979	0.001	0.017	0.003
10	0.001	0.637	0.108	0.254
11	0.12	0.517	0.215	0.148
12	0.205	0.214	0.187	0.395

PWM

	A	C	G	T
01	0.042	-0.106	0.249	-0.254
02	-0.365	-0.981	-0.608	0.87
03	-2.108	-4.265	-2.815	1.336
04	-5.049	-5.595	-5.871	1.383
05	-0.952	-6.887	-6.887	1.284
06	1.385	-6.887	-6.887	-6.045
07	-6.522	1.219	-6.887	-0.486
08	-6.522	-5.871	1.356	-2.158
09	1.364	-5.122	-2.689	-4.234
10	-4.982	0.935	-0.839	0.015
11	-0.732	0.726	-0.153	-0.522
12	-0.199	-0.156	-0.292	0.456

Standard thresholds

P-value	Threshold
0.001	2.34511
0.0005	3.82799
0.0001	6.988205