HXC9.H12INVITRO.0.P.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXC9.H12INVITRO.0.P.B
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	B

Motif length	13
Consensus	bhTTTATKRYYhh
GC content	34.44%
Information content (bits; total / per base)	10.933 / 0.841
Data sources	ChIP-Seq
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
Human	1 (7)	0.765	0.801	0.623	0.659	0.816	0.836	2.506	2.59	59.538	80.444
Mouse	3 (19)	0.802	0.814	0.664	0.689	0.807	0.844	2.596	2.7	101.523	127.06

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.971	0.952	0.948	0.922	0.9	0.871
Overall, 2 experiments	best	0.972	0.953	0.949	0.924	0.905	0.874
Methyl HT-SELEX, 1 experiments	median	0.972	0.953	0.949	0.924	0.895	0.868
Methyl HT-SELEX, 1 experiments	best	0.972	0.953	0.949	0.924	0.895	0.868
Non-Methyl HT-SELEX, 1 experiments	median	0.97	0.95	0.947	0.921	0.905	0.874
Non-Methyl HT-SELEX, 1 experiments	best	0.97	0.95	0.947	0.921	0.905	0.874

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.H12INVITRO.0.P.B.pcm
PWM	HXC9.H12INVITRO.0.P.B.pwm
PFM	HXC9.H12INVITRO.0.P.B.pfm
Alignment	HXC9.H12INVITRO.0.P.B.words.tsv
Threshold to P-value map	HXC9.H12INVITRO.0.P.B.thr
Motif in other formats
JASPAR format	HXC9.H12INVITRO.0.P.B_jaspar_format.txt
MEME format	HXC9.H12INVITRO.0.P.B_meme_format.meme
Transfac format	HXC9.H12INVITRO.0.P.B_transfac_format.txt
Homer format	HXC9.H12INVITRO.0.P.B_homer_format_0.001.txt HXC9.H12INVITRO.0.P.B_homer_format_0.0005.txt HXC9.H12INVITRO.0.P.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	156.0	187.0	425.0	232.0
02	408.0	110.0	53.0	429.0
03	13.0	8.0	30.0	949.0
04	5.0	10.0	1.0	984.0
05	98.0	41.0	46.0	815.0
06	993.0	2.0	4.0	1.0
07	11.0	42.0	27.0	920.0
08	106.0	3.0	489.0	402.0
09	150.0	17.0	713.0	120.0
10	42.0	601.0	173.0	184.0
11	79.0	517.0	74.0	330.0
12	199.0	336.0	104.0	361.0
13	172.0	303.0	161.0	364.0

PFM

	A	C	G	T
01	0.156	0.187	0.425	0.232
02	0.408	0.11	0.053	0.429
03	0.013	0.008	0.03	0.949
04	0.005	0.01	0.001	0.984
05	0.098	0.041	0.046	0.815
06	0.993	0.002	0.004	0.001
07	0.011	0.042	0.027	0.92
08	0.106	0.003	0.489	0.402
09	0.15	0.017	0.713	0.12
10	0.042	0.601	0.173	0.184
11	0.079	0.517	0.074	0.33
12	0.199	0.336	0.104	0.361
13	0.172	0.303	0.161	0.364

PWM

	A	C	G	T
01	-0.467	-0.288	0.528	-0.074
02	0.487	-0.812	-1.526	0.537
03	-2.839	-3.253	-2.071	1.329
04	-3.622	-3.066	-4.525	1.365
05	-0.926	-1.774	-1.663	1.177
06	1.374	-4.213	-3.783	-4.525
07	-2.985	-1.75	-2.171	1.298
08	-0.849	-3.975	0.668	0.472
09	-0.506	-2.598	1.044	-0.727
10	-1.75	0.873	-0.365	-0.304
11	-1.137	0.723	-1.201	0.276
12	-0.226	0.294	-0.867	0.365
13	-0.371	0.191	-0.436	0.374

Standard thresholds

P-value	Threshold
0.001	4.50676
0.0005	5.45616
0.0001	7.36932