HXD13.H12INVITRO.0.PS.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXD13.H12INVITRO.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	11
Consensus	ndTTTATKRbn
GC content	30.22%
Information content (bits; total / per base)	9.657 / 0.878
Data sources	ChIP-Seq + HT-SELEX
Aligned words	8466

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)	0.857	0.872	0.721	0.75	0.834	0.84	2.466	2.513	82.638	104.041

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.805	0.755	0.706	0.676	0.617	0.613
Overall, 5 experiments	best	0.975	0.953	0.96	0.936	0.914	0.888
Methyl HT-SELEX, 1 experiments	median	0.968	0.94	0.939	0.91	0.821	0.812
Methyl HT-SELEX, 1 experiments	best	0.968	0.94	0.939	0.91	0.821	0.812
Non-Methyl HT-SELEX, 4 experiments	median	0.777	0.736	0.678	0.653	0.601	0.597
Non-Methyl HT-SELEX, 4 experiments	best	0.975	0.953	0.96	0.936	0.914	0.888

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.0.PS.A.pcm
PWM	HXD13.H12INVITRO.0.PS.A.pwm
PFM	HXD13.H12INVITRO.0.PS.A.pfm
Alignment	HXD13.H12INVITRO.0.PS.A.words.tsv
Threshold to P-value map	HXD13.H12INVITRO.0.PS.A.thr
Motif in other formats
JASPAR format	HXD13.H12INVITRO.0.PS.A_jaspar_format.txt
MEME format	HXD13.H12INVITRO.0.PS.A_meme_format.meme
Transfac format	HXD13.H12INVITRO.0.PS.A_transfac_format.txt
Homer format	HXD13.H12INVITRO.0.PS.A_homer_format_0.001.txt HXD13.H12INVITRO.0.PS.A_homer_format_0.0005.txt HXD13.H12INVITRO.0.PS.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2194.75	1618.75	2230.75	2421.75
02	1264.25	822.25	1957.25	4422.25
03	315.0	94.0	291.0	7766.0
04	159.0	29.0	99.0	8179.0
05	1488.0	59.0	15.0	6904.0
06	8462.0	0.0	4.0	0.0
07	11.0	2509.0	1.0	5945.0
08	449.0	109.0	5036.0	2872.0
09	5401.0	271.0	2404.0	390.0
10	736.75	1609.75	4823.75	1295.75
11	2008.75	2144.75	2016.75	2295.75

PFM

	A	C	G	T
01	0.259	0.191	0.263	0.286
02	0.149	0.097	0.231	0.522
03	0.037	0.011	0.034	0.917
04	0.019	0.003	0.012	0.966
05	0.176	0.007	0.002	0.815
06	1.0	0.0	0.0	0.0
07	0.001	0.296	0.0	0.702
08	0.053	0.013	0.595	0.339
09	0.638	0.032	0.284	0.046
10	0.087	0.19	0.57	0.153
11	0.237	0.253	0.238	0.271

PWM

	A	C	G	T
01	0.036	-0.268	0.053	0.135
02	-0.515	-0.944	-0.078	0.736
03	-1.899	-3.092	-1.978	1.299
04	-2.576	-4.216	-3.041	1.351
05	-0.352	-3.543	-4.81	1.182
06	1.385	-6.843	-5.824	-6.843
07	-5.074	0.17	-6.477	1.032
08	-1.547	-2.947	0.866	0.305
09	0.936	-2.048	0.127	-1.687
10	-1.053	-0.273	0.823	-0.49
11	-0.052	0.013	-0.048	0.081

Standard thresholds

P-value	Threshold
0.001	4.918385
0.0005	5.876625
0.0001	7.501445