HXD13.H14RSNP.0.PS.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD13.H14RSNP.0.PS.D
Gene (human)	HOXD13 (GeneCards)
Gene synonyms (human)	HOX4I
Gene (mouse)	Hoxd13
Gene synonyms (mouse)	Hox-4.8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	11
Consensus	nKTTTATdRSn
GC content	30.6%
Information content (bits; total / per base)	10.608 / 0.964
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1001
Previous names	HXD13.H12RSNP.0.PS.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	1 (7)	0.879	0.898	0.756	0.795	0.844	0.85	2.503	2.552	91.678	119.268

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.81	0.759	0.708	0.679	0.609	0.612
Overall, 5 experiments	best	0.962	0.939	0.942	0.911	0.901	0.867
Methyl HT-SELEX, 1 experiments	median	0.904	0.856	0.872	0.82	0.775	0.747
Methyl HT-SELEX, 1 experiments	best	0.904	0.856	0.872	0.82	0.775	0.747
Non-Methyl HT-SELEX, 4 experiments	median	0.783	0.739	0.681	0.654	0.595	0.596
Non-Methyl HT-SELEX, 4 experiments	best	0.962	0.939	0.942	0.911	0.901	0.867

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: 3.1.1.8.17
HGNC	HGNC:5136
MGI	MGI:96205
EntrezGene (human)	GeneID:3239 (SSTAR profile)
EntrezGene (mouse)	GeneID:15433 (SSTAR profile)
UniProt ID (human)	HXD13_HUMAN
UniProt ID (mouse)	HXD13_MOUSE
UniProt AC (human)	P35453 (TFClass)
UniProt AC (mouse)	P70217 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	4
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	HXD13.H14RSNP.0.PS.D.pcm
PWM	HXD13.H14RSNP.0.PS.D.pwm
PFM	HXD13.H14RSNP.0.PS.D.pfm
Threshold to P-value map	HXD13.H14RSNP.0.PS.D.thr
Motif in other formats
JASPAR format	HXD13.H14RSNP.0.PS.D_jaspar_format.txt
MEME format	HXD13.H14RSNP.0.PS.D_meme_format.meme
Transfac format	HXD13.H14RSNP.0.PS.D_transfac_format.txt
Homer format	HXD13.H14RSNP.0.PS.D_homer_format_0.001.txt HXD13.H14RSNP.0.PS.D_homer_format_0.0005.txt HXD13.H14RSNP.0.PS.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	200.0	156.0	354.0	291.0
02	91.0	110.0	143.0	657.0
03	3.0	1.0	5.0	992.0
04	2.0	2.0	2.0	995.0
05	144.0	24.0	8.0	825.0
06	993.0	3.0	2.0	3.0
07	29.0	111.0	2.0	859.0
08	290.0	2.0	345.0	364.0
09	306.0	3.0	627.0	65.0
10	86.0	279.0	588.0	48.0
11	216.0	374.0	228.0	183.0

PFM

	A	C	G	T
01	0.2	0.156	0.354	0.291
02	0.091	0.11	0.143	0.656
03	0.003	0.001	0.005	0.991
04	0.002	0.002	0.002	0.994
05	0.144	0.024	0.008	0.824
06	0.992	0.003	0.002	0.003
07	0.029	0.111	0.002	0.858
08	0.29	0.002	0.345	0.364
09	0.306	0.003	0.626	0.065
10	0.086	0.279	0.587	0.048
11	0.216	0.374	0.228	0.183

PWM

	A	C	G	T
01	-0.222	-0.468	0.345	0.15
02	-1.0	-0.813	-0.554	0.961
03	-3.976	-4.526	-3.623	1.372
04	-4.214	-4.214	-4.214	1.375
05	-0.548	-2.282	-3.254	1.188
06	1.373	-3.976	-4.214	-3.976
07	-2.104	-0.804	-4.214	1.228
08	0.146	-4.214	0.319	0.373
09	0.2	-3.976	0.914	-1.329
10	-1.055	0.108	0.85	-1.623
11	-0.146	0.4	-0.092	-0.31

Standard thresholds

P-value	Threshold
0.001	4.63346
0.0005	5.648735
0.0001	7.54083