HXD11.H12INVIVO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD11.H12INVIVO.0.PS.A
Gene (human)	HOXD11 (GeneCards)
Gene synonyms (human)	HOX4F
Gene (mouse)	Hoxd11
Gene synonyms (mouse)	Hox-4.6, Hoxd-11
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	13
Consensus	dRnTTWATGRbbb
GC content	39.59%
Information content (bits; total / per base)	9.843 / 0.757
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)	0.852	0.858	0.777	0.786	0.861	0.867	3.227	3.263	191.77	201.959

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.772	0.725	0.726	0.69	0.667	0.646
Overall, 4 experiments	best	0.944	0.907	0.919	0.878	0.862	0.824
Methyl HT-SELEX, 1 experiments	median	0.912	0.862	0.872	0.82	0.789	0.754
Methyl HT-SELEX, 1 experiments	best	0.912	0.862	0.872	0.82	0.789	0.754
Non-Methyl HT-SELEX, 3 experiments	median	0.631	0.588	0.58	0.559	0.544	0.538
Non-Methyl HT-SELEX, 3 experiments	best	0.944	0.907	0.919	0.878	0.862	0.824

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: 3.1.1.8.11
HGNC	HGNC:5134
MGI	MGI:96203
EntrezGene (human)	GeneID:3237 (SSTAR profile)
EntrezGene (mouse)	GeneID:15431 (SSTAR profile)
UniProt ID (human)	HXD11_HUMAN
UniProt ID (mouse)	HXD11_MOUSE
UniProt AC (human)	P31277 (TFClass)
UniProt AC (mouse)	P23813 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 1 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	HXD11.H12INVIVO.0.PS.A.pcm
PWM	HXD11.H12INVIVO.0.PS.A.pwm
PFM	HXD11.H12INVIVO.0.PS.A.pfm
Alignment	HXD11.H12INVIVO.0.PS.A.words.tsv
Threshold to P-value map	HXD11.H12INVIVO.0.PS.A.thr
Motif in other formats
JASPAR format	HXD11.H12INVIVO.0.PS.A_jaspar_format.txt
MEME format	HXD11.H12INVIVO.0.PS.A_meme_format.meme
Transfac format	HXD11.H12INVIVO.0.PS.A_transfac_format.txt
Homer format	HXD11.H12INVIVO.0.PS.A_homer_format_0.001.txt HXD11.H12INVIVO.0.PS.A_homer_format_0.0005.txt HXD11.H12INVIVO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	448.0	61.0	219.0	272.0
02	256.0	70.0	565.0	109.0
03	289.0	153.0	261.0	297.0
04	9.0	38.0	58.0	895.0
05	16.0	30.0	10.0	944.0
06	472.0	54.0	56.0	418.0
07	964.0	17.0	15.0	4.0
08	6.0	52.0	21.0	921.0
09	38.0	11.0	812.0	139.0
10	397.0	17.0	517.0	69.0
11	108.0	346.0	381.0	165.0
12	88.0	484.0	266.0	162.0
13	93.0	500.0	133.0	274.0

PFM

	A	C	G	T
01	0.448	0.061	0.219	0.272
02	0.256	0.07	0.565	0.109
03	0.289	0.153	0.261	0.297
04	0.009	0.038	0.058	0.895
05	0.016	0.03	0.01	0.944
06	0.472	0.054	0.056	0.418
07	0.964	0.017	0.015	0.004
08	0.006	0.052	0.021	0.921
09	0.038	0.011	0.812	0.139
10	0.397	0.017	0.517	0.069
11	0.108	0.346	0.381	0.165
12	0.088	0.484	0.266	0.162
13	0.093	0.5	0.133	0.274

PWM

	A	C	G	T
01	0.58	-1.39	-0.131	0.084
02	0.024	-1.255	0.812	-0.821
03	0.144	-0.487	0.043	0.171
04	-3.156	-1.846	-1.439	1.27
05	-2.653	-2.071	-3.066	1.324
06	0.632	-1.508	-1.473	0.511
07	1.345	-2.598	-2.711	-3.783
08	-3.484	-1.544	-2.405	1.299
09	-1.846	-2.985	1.173	-0.582
10	0.46	-2.598	0.723	-1.27
11	-0.83	0.323	0.419	-0.412
12	-1.032	0.657	0.062	-0.43
13	-0.977	0.69	-0.625	0.091

Standard thresholds

P-value	Threshold
0.001	4.75676
0.0005	5.59821
0.0001	7.32726