HXD13.H12INVITRO.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD13.H12INVITRO.1.SM.B
Gene (human)	HOXD13 (GeneCards)
Gene synonyms (human)	HOX4I
Gene (mouse)	Hoxd13
Gene synonyms (mouse)	Hox-4.8
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	11
Consensus	ndTTTACGASn
GC content	38.95%
Information content (bits; total / per base)	12.429 / 1.13
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8318

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)	0.851	0.862	0.708	0.747	0.81	0.821	2.341	2.429	74.018	82.553

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.775	0.737	0.685	0.659	0.613	0.605
Overall, 5 experiments	best	0.994	0.991	0.967	0.956	0.908	0.892
Methyl HT-SELEX, 1 experiments	median	0.994	0.991	0.962	0.954	0.836	0.84
Methyl HT-SELEX, 1 experiments	best	0.994	0.991	0.962	0.954	0.836	0.84
Non-Methyl HT-SELEX, 4 experiments	median	0.748	0.719	0.659	0.639	0.596	0.589
Non-Methyl HT-SELEX, 4 experiments	best	0.99	0.985	0.967	0.956	0.908	0.892

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

PCM	HXD13.H12INVITRO.1.SM.B.pcm
PWM	HXD13.H12INVITRO.1.SM.B.pwm
PFM	HXD13.H12INVITRO.1.SM.B.pfm
Alignment	HXD13.H12INVITRO.1.SM.B.words.tsv
Threshold to P-value map	HXD13.H12INVITRO.1.SM.B.thr
Motif in other formats
JASPAR format	HXD13.H12INVITRO.1.SM.B_jaspar_format.txt
MEME format	HXD13.H12INVITRO.1.SM.B_meme_format.meme
Transfac format	HXD13.H12INVITRO.1.SM.B_transfac_format.txt
Homer format	HXD13.H12INVITRO.1.SM.B_homer_format_0.001.txt HXD13.H12INVITRO.1.SM.B_homer_format_0.0005.txt HXD13.H12INVITRO.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2048.75	1588.75	2738.75	1941.75
02	1433.0	875.0	1923.0	4087.0
03	248.0	47.0	298.0	7725.0
04	92.0	24.0	22.0	8180.0
05	906.0	48.0	6.0	7358.0
06	8318.0	0.0	0.0	0.0
07	0.0	6632.0	1.0	1685.0
08	249.0	10.0	7841.0	218.0
09	7523.0	77.0	658.0	60.0
10	224.0	993.0	6407.0	694.0
11	1601.5	2691.5	2758.5	1266.5

PFM

	A	C	G	T
01	0.246	0.191	0.329	0.233
02	0.172	0.105	0.231	0.491
03	0.03	0.006	0.036	0.929
04	0.011	0.003	0.003	0.983
05	0.109	0.006	0.001	0.885
06	1.0	0.0	0.0	0.0
07	0.0	0.797	0.0	0.203
08	0.03	0.001	0.943	0.026
09	0.904	0.009	0.079	0.007
10	0.027	0.119	0.77	0.083
11	0.193	0.324	0.332	0.152

PWM

	A	C	G	T
01	-0.015	-0.269	0.275	-0.068
02	-0.372	-0.864	-0.078	0.675
03	-2.118	-3.744	-1.936	1.312
04	-3.095	-4.373	-4.452	1.369
05	-0.829	-3.724	-5.53	1.263
06	1.385	-6.827	-6.827	-6.827
07	-6.827	1.159	-6.46	-0.21
08	-2.114	-5.135	1.326	-2.246
09	1.285	-3.268	-1.148	-3.51
10	-2.219	-0.738	1.125	-1.095
11	-0.261	0.258	0.282	-0.495

Standard thresholds

P-value	Threshold
0.001	3.679365
0.0005	4.85848
0.0001	7.264295