HXB8.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HXB8.H12INVITRO.0.PSM.A
Gene (human)	HOXB8 (GeneCards)
Gene synonyms (human)	HOX2D
Gene (mouse)	Hoxb8
Gene synonyms (mouse)	Hox-2.4, Hoxb-8
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nhvbTAATKRbn
GC content	36.95%
Information content (bits; total / per base)	10.558 / 0.88
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9673

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 (5)	0.761	0.786	0.629	0.649	0.64	0.667	1.552	1.623	27.252	42.301

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 2 experiments	median	0.934	0.898	0.895	0.854	0.834	0.795
Overall, 2 experiments	best	0.953	0.925	0.924	0.889	0.869	0.833
Methyl HT-SELEX, 1 experiments	median	0.915	0.871	0.866	0.819	0.799	0.758
Methyl HT-SELEX, 1 experiments	best	0.915	0.871	0.866	0.819	0.799	0.758
Non-Methyl HT-SELEX, 1 experiments	median	0.953	0.925	0.924	0.889	0.869	0.833
Non-Methyl HT-SELEX, 1 experiments	best	0.953	0.925	0.924	0.889	0.869	0.833

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	HOX8 {3.1.1.7} (TFClass)
TFClass ID	TFClass: 3.1.1.7.1
HGNC	HGNC:5119
MGI	MGI:96189
EntrezGene (human)	GeneID:3218 (SSTAR profile)
EntrezGene (mouse)	GeneID:15416 (SSTAR profile)
UniProt ID (human)	HXB8_HUMAN
UniProt ID (mouse)	HXB8_MOUSE
UniProt AC (human)	P17481 (TFClass)
UniProt AC (mouse)	P09632 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	1 human, 0 mouse
HT-SELEX	1
Methyl-HT-SELEX	1

PCM	HXB8.H12INVITRO.0.PSM.A.pcm
PWM	HXB8.H12INVITRO.0.PSM.A.pwm
PFM	HXB8.H12INVITRO.0.PSM.A.pfm
Alignment	HXB8.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	HXB8.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	HXB8.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	HXB8.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	HXB8.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	HXB8.H12INVITRO.0.PSM.A_homer_format_0.001.txt HXB8.H12INVITRO.0.PSM.A_homer_format_0.0005.txt HXB8.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2482.5	2356.5	2423.5	2410.5
02	1873.75	4139.75	1652.75	2006.75
03	2781.0	2582.0	3678.0	632.0
04	1080.0	1454.0	1651.0	5488.0
05	0.0	5.0	1.0	9667.0
06	9673.0	0.0	0.0	0.0
07	9673.0	0.0	0.0	0.0
08	0.0	102.0	1.0	9570.0
09	24.0	70.0	4949.0	4630.0
10	4144.0	119.0	4925.0	485.0
11	861.75	5643.75	1831.75	1335.75
12	2132.25	3146.25	2159.25	2235.25

PFM

	A	C	G	T
01	0.257	0.244	0.251	0.249
02	0.194	0.428	0.171	0.207
03	0.288	0.267	0.38	0.065
04	0.112	0.15	0.171	0.567
05	0.0	0.001	0.0	0.999
06	1.0	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.011	0.0	0.989
09	0.002	0.007	0.512	0.479
10	0.428	0.012	0.509	0.05
11	0.089	0.583	0.189	0.138
12	0.22	0.325	0.223	0.231

PWM

	A	C	G	T
01	0.026	-0.026	0.002	-0.003
02	-0.255	0.537	-0.38	-0.186
03	0.14	0.065	0.419	-1.339
04	-0.805	-0.508	-0.381	0.819
05	-6.961	-5.805	-6.6	1.385
06	1.386	-6.961	-6.961	-6.961
07	1.386	-6.961	-6.961	-6.961
08	-6.961	-3.145	-6.6	1.375
09	-4.522	-3.511	0.716	0.649
10	0.538	-2.994	0.711	-1.603
11	-1.03	0.847	-0.277	-0.593
12	-0.126	0.263	-0.113	-0.079

Standard thresholds

P-value	Threshold
0.001	4.753685
0.0005	6.030275
0.0001	7.65123