HXD13.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD13.H12INVIVO.0.PS.A
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	A

Motif length	12
Consensus	nKTTTATKRSbh
GC content	32.7%
Information content (bits; total / per base)	10.66 / 0.888
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1000

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)	0.875	0.89	0.753	0.786	0.849	0.856	2.564	2.645	92.444	112.194

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.805	0.756	0.699	0.673	0.602	0.607
Overall, 5 experiments	best	0.961	0.937	0.938	0.907	0.885	0.853
Methyl HT-SELEX, 1 experiments	median	0.91	0.862	0.873	0.822	0.769	0.744
Methyl HT-SELEX, 1 experiments	best	0.91	0.862	0.873	0.822	0.769	0.744
Non-Methyl HT-SELEX, 4 experiments	median	0.775	0.733	0.673	0.649	0.588	0.592
Non-Methyl HT-SELEX, 4 experiments	best	0.961	0.937	0.938	0.907	0.885	0.853

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.H12INVIVO.0.PS.A.pcm
PWM	HXD13.H12INVIVO.0.PS.A.pwm
PFM	HXD13.H12INVIVO.0.PS.A.pfm
Alignment	HXD13.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	HXD13.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	HXD13.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	HXD13.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	HXD13.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	HXD13.H12INVIVO.0.PS.A_homer_format_0.001.txt HXD13.H12INVIVO.0.PS.A_homer_format_0.0005.txt HXD13.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	218.0	174.0	362.0	246.0
02	88.0	95.0	154.0	663.0
03	2.0	3.0	8.0	987.0
04	1.0	1.0	2.0	996.0
05	113.0	37.0	8.0	842.0
06	976.0	13.0	6.0	5.0
07	22.0	82.0	3.0	893.0
08	207.0	6.0	467.0	320.0
09	347.0	2.0	551.0	100.0
10	129.0	218.0	602.0	51.0
11	138.0	399.0	275.0	188.0
12	200.0	333.0	123.0	344.0

PFM

	A	C	G	T
01	0.218	0.174	0.362	0.246
02	0.088	0.095	0.154	0.663
03	0.002	0.003	0.008	0.987
04	0.001	0.001	0.002	0.996
05	0.113	0.037	0.008	0.842
06	0.976	0.013	0.006	0.005
07	0.022	0.082	0.003	0.893
08	0.207	0.006	0.467	0.32
09	0.347	0.002	0.551	0.1
10	0.129	0.218	0.602	0.051
11	0.138	0.399	0.275	0.188
12	0.2	0.333	0.123	0.344

PWM

	A	C	G	T
01	-0.136	-0.359	0.368	-0.016
02	-1.032	-0.956	-0.48	0.971
03	-4.213	-3.975	-3.253	1.368
04	-4.525	-4.525	-4.213	1.377
05	-0.786	-1.872	-3.253	1.209
06	1.357	-2.839	-3.484	-3.622
07	-2.362	-1.101	-3.975	1.268
08	-0.187	-3.484	0.622	0.245
09	0.326	-4.213	0.787	-0.906
10	-0.655	-0.136	0.875	-1.563
11	-0.589	0.465	0.095	-0.283
12	-0.221	0.285	-0.702	0.317

Standard thresholds

P-value	Threshold
0.001	4.58301
0.0005	5.60496
0.0001	7.503475