HXA13.H12INVIVO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXA13.H12INVIVO.0.P.B
Gene (human)	HOXA13 (GeneCards)
Gene synonyms (human)	HOX1J
Gene (mouse)	Hoxa13
Gene synonyms (mouse)	Hox-1.10
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	B

Motif length	11
Consensus	ddTTTTATKRG
GC content	23.15%
Information content (bits; total / per base)	14.05 / 1.277
Data sources	ChIP-Seq
Aligned words	1006

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	4 (27)	0.928	0.97	0.879	0.929	0.906	0.945	3.477	3.795	153.77	393.569

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 5 experiments	median	0.968	0.929	0.967	0.936	0.935	0.905
Overall, 5 experiments	best	0.979	0.959	0.978	0.959	0.963	0.942
Methyl HT-SELEX, 2 experiments	median	0.965	0.928	0.957	0.924	0.907	0.879
Methyl HT-SELEX, 2 experiments	best	0.968	0.929	0.967	0.936	0.935	0.905
Non-Methyl HT-SELEX, 3 experiments	median	0.975	0.954	0.967	0.944	0.944	0.917
Non-Methyl HT-SELEX, 3 experiments	best	0.979	0.959	0.978	0.959	0.963	0.942

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: 3.1.1.8.14
HGNC	HGNC:5102
MGI	MGI:96173
EntrezGene (human)	GeneID:3209 (SSTAR profile)
EntrezGene (mouse)	GeneID:15398 (SSTAR profile)
UniProt ID (human)	HXA13_HUMAN
UniProt ID (mouse)	HXA13_MOUSE
UniProt AC (human)	P31271 (TFClass)
UniProt AC (mouse)	Q62424 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	2

PCM	HXA13.H12INVIVO.0.P.B.pcm
PWM	HXA13.H12INVIVO.0.P.B.pwm
PFM	HXA13.H12INVIVO.0.P.B.pfm
Alignment	HXA13.H12INVIVO.0.P.B.words.tsv
Threshold to P-value map	HXA13.H12INVIVO.0.P.B.thr
Motif in other formats
JASPAR format	HXA13.H12INVIVO.0.P.B_jaspar_format.txt
MEME format	HXA13.H12INVIVO.0.P.B_meme_format.meme
Transfac format	HXA13.H12INVIVO.0.P.B_transfac_format.txt
Homer format	HXA13.H12INVIVO.0.P.B_homer_format_0.001.txt HXA13.H12INVIVO.0.P.B_homer_format_0.0005.txt HXA13.H12INVIVO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	540.0	66.0	157.0	243.0
02	299.0	71.0	215.0	421.0
03	34.0	10.0	40.0	922.0
04	0.0	0.0	0.0	1006.0
05	5.0	0.0	1.0	1000.0
06	101.0	0.0	0.0	905.0
07	1005.0	0.0	0.0	1.0
08	1.0	105.0	1.0	899.0
09	41.0	0.0	437.0	528.0
10	522.0	0.0	474.0	10.0
11	16.0	112.0	873.0	5.0

PFM

	A	C	G	T
01	0.537	0.066	0.156	0.242
02	0.297	0.071	0.214	0.418
03	0.034	0.01	0.04	0.917
04	0.0	0.0	0.0	1.0
05	0.005	0.0	0.001	0.994
06	0.1	0.0	0.0	0.9
07	0.999	0.0	0.0	0.001
08	0.001	0.104	0.001	0.894
09	0.041	0.0	0.434	0.525
10	0.519	0.0	0.471	0.01
11	0.016	0.111	0.868	0.005

PWM

	A	C	G	T
01	0.76	-1.319	-0.467	-0.034
02	0.172	-1.248	-0.156	0.512
03	-1.958	-3.072	-1.803	1.294
04	-4.987	-4.987	-4.987	1.381
05	-3.628	-4.987	-4.531	1.375
06	-0.902	-4.987	-4.987	1.276
07	1.38	-4.987	-4.987	-4.531
08	-4.531	-0.864	-4.531	1.269
09	-1.779	-4.987	0.55	0.738
10	0.727	-4.987	0.631	-3.072
11	-2.659	-0.8	1.24	-3.628

Standard thresholds

P-value	Threshold
0.001	2.686375
0.0005	4.049415
0.0001	6.826935