HXD11.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD11.H12INVITRO.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	10
Consensus	nWTTTATGRb
GC content	28.26%
Information content (bits; total / per base)	10.495 / 1.049
Data sources	ChIP-Seq + HT-SELEX
Aligned words	1923

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)	0.743	0.745	0.597	0.605	0.821	0.828	2.623	2.643	102.398	109.658

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.831	0.792	0.774	0.746	0.703	0.691
Overall, 4 experiments	best	0.98	0.959	0.967	0.946	0.923	0.902
Methyl HT-SELEX, 1 experiments	median	0.963	0.93	0.928	0.894	0.841	0.819
Methyl HT-SELEX, 1 experiments	best	0.963	0.93	0.928	0.894	0.841	0.819
Non-Methyl HT-SELEX, 3 experiments	median	0.699	0.653	0.619	0.598	0.565	0.562
Non-Methyl HT-SELEX, 3 experiments	best	0.98	0.959	0.967	0.946	0.923	0.902

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.H12INVITRO.0.PS.A.pcm
PWM	HXD11.H12INVITRO.0.PS.A.pwm
PFM	HXD11.H12INVITRO.0.PS.A.pfm
Alignment	HXD11.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	HXD11.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	HXD11.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	HXD11.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	HXD11.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	HXD11.H12INVITRO.0.PS.A_homer_format_0.001.txt HXD11.H12INVITRO.0.PS.A_homer_format_0.0005.txt HXD11.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	455.0	471.0	389.0	608.0
02	211.5	187.5	194.5	1329.5
03	25.0	3.0	1.0	1894.0
04	0.0	0.0	0.0	1923.0
05	495.0	0.0	0.0	1428.0
06	1923.0	0.0	0.0	0.0
07	4.0	632.0	0.0	1287.0
08	21.0	81.0	1640.0	181.0
09	1075.5	145.5	514.5	187.5
10	196.75	552.75	622.75	550.75

PFM

	A	C	G	T
01	0.237	0.245	0.202	0.316
02	0.11	0.098	0.101	0.691
03	0.013	0.002	0.001	0.985
04	0.0	0.0	0.0	1.0
05	0.257	0.0	0.0	0.743
06	1.0	0.0	0.0	0.0
07	0.002	0.329	0.0	0.669
08	0.011	0.042	0.853	0.094
09	0.559	0.076	0.268	0.098
10	0.102	0.287	0.324	0.286

PWM

	A	C	G	T
01	-0.055	-0.02	-0.211	0.234
02	-0.816	-0.935	-0.899	1.015
03	-2.888	-4.592	-5.118	1.368
04	-5.542	-5.542	-5.542	1.383
05	0.029	-5.542	-5.542	1.086
06	1.383	-5.542	-5.542	-5.542
07	-4.406	0.273	-5.542	0.982
08	-3.049	-1.762	1.224	-0.97
09	0.803	-1.186	0.068	-0.935
10	-0.888	0.139	0.258	0.135

Standard thresholds

P-value	Threshold
0.001	4.752805
0.0005	5.817685
0.0001	7.571575