HXC9.H12RSNP.0.P.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC9.H12RSNP.0.P.D
Gene (human)	HOXC9 (GeneCards)
Gene synonyms (human)	HOX3B
Gene (mouse)	Hoxc9
Gene synonyms (mouse)	Hox-3.2, Hoxc-9
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	12
Consensus	WRATTTAYdRbh
GC content	32.0%
Information content (bits; total / per base)	10.986 / 0.915
Data sources	ChIP-Seq
Aligned words	993

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
Human	1 (7)	0.751	0.773	0.587	0.619	0.796	0.8	2.342	2.364	55.018	61.523
Mouse	3 (19)	0.868	0.89	0.769	0.819	0.86	0.879	3.09	3.359	117.824	171.62

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.913	0.862	0.883	0.83	0.826	0.779
Overall, 2 experiments	best	0.923	0.875	0.893	0.843	0.831	0.788
Methyl HT-SELEX, 1 experiments	median	0.923	0.875	0.893	0.843	0.831	0.788
Methyl HT-SELEX, 1 experiments	best	0.923	0.875	0.893	0.843	0.831	0.788
Non-Methyl HT-SELEX, 1 experiments	median	0.904	0.85	0.873	0.817	0.82	0.769
Non-Methyl HT-SELEX, 1 experiments	best	0.904	0.85	0.873	0.817	0.82	0.769

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: 3.1.1.8.3
HGNC	HGNC:5130
MGI	MGI:96199
EntrezGene (human)	GeneID:3225 (SSTAR profile)
EntrezGene (mouse)	GeneID:15427 (SSTAR profile)
UniProt ID (human)	HXC9_HUMAN
UniProt ID (mouse)	HXC9_MOUSE
UniProt AC (human)	P31274 (TFClass)
UniProt AC (mouse)	P09633 (TFClass)
GRECO-DB-TF	yes

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

PCM	HXC9.H12RSNP.0.P.D.pcm
PWM	HXC9.H12RSNP.0.P.D.pwm
PFM	HXC9.H12RSNP.0.P.D.pfm
Alignment	HXC9.H12RSNP.0.P.D.words.tsv
Threshold to P-value map	HXC9.H12RSNP.0.P.D.thr
Motif in other formats
JASPAR format	HXC9.H12RSNP.0.P.D_jaspar_format.txt
MEME format	HXC9.H12RSNP.0.P.D_meme_format.meme
Transfac format	HXC9.H12RSNP.0.P.D_transfac_format.txt
Homer format	HXC9.H12RSNP.0.P.D_homer_format_0.001.txt HXC9.H12RSNP.0.P.D_homer_format_0.0005.txt HXC9.H12RSNP.0.P.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	258.0	15.0	127.0	593.0
02	179.0	21.0	697.0	96.0
03	830.0	36.0	24.0	103.0
04	45.0	6.0	17.0	925.0
05	34.0	6.0	6.0	947.0
06	49.0	53.0	43.0	848.0
07	968.0	5.0	17.0	3.0
08	30.0	205.0	34.0	724.0
09	192.0	21.0	483.0	297.0
10	172.0	60.0	672.0	89.0
11	97.0	538.0	174.0	184.0
12	178.0	400.0	153.0	262.0

PFM

	A	C	G	T
01	0.26	0.015	0.128	0.597
02	0.18	0.021	0.702	0.097
03	0.836	0.036	0.024	0.104
04	0.045	0.006	0.017	0.932
05	0.034	0.006	0.006	0.954
06	0.049	0.053	0.043	0.854
07	0.975	0.005	0.017	0.003
08	0.03	0.206	0.034	0.729
09	0.193	0.021	0.486	0.299
10	0.173	0.06	0.677	0.09
11	0.098	0.542	0.175	0.185
12	0.179	0.403	0.154	0.264

PWM

	A	C	G	T
01	0.038	-2.704	-0.664	0.867
02	-0.324	-2.398	1.028	-0.939
03	1.202	-1.891	-2.274	-0.87
04	-1.677	-3.477	-2.591	1.31
05	-1.946	-3.477	-3.477	1.334
06	-1.595	-1.519	-1.721	1.224
07	1.356	-3.616	-2.591	-3.968
08	-2.064	-0.19	-1.946	1.066
09	-0.255	-2.398	0.662	0.178
10	-0.364	-1.399	0.991	-1.014
11	-0.929	0.77	-0.352	-0.297
12	-0.33	0.474	-0.48	0.054

Standard thresholds

P-value	Threshold
0.001	4.49017
0.0005	5.394165
0.0001	7.249495