HMBX1.H12INVIVO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HMBX1.H12INVIVO.0.PSM.A
Gene (human)	HMBOX1 (GeneCards)
Gene synonyms (human)	HOT1, TAH1
Gene (mouse)	Hmbox1
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	9
Consensus	dvYTAGTbA
GC content	39.5%
Information content (bits; total / per base)	9.438 / 1.049
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
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	3 (21)	0.814	0.868	0.66	0.731	0.74	0.784	2.071	2.274	86.553	113.432

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.856	0.838	0.796	0.789	0.757	0.755
Overall, 4 experiments	best	0.99	0.983	0.981	0.971	0.963	0.945
Methyl HT-SELEX, 2 experiments	median	0.858	0.841	0.797	0.792	0.757	0.755
Methyl HT-SELEX, 2 experiments	best	0.99	0.983	0.981	0.971	0.958	0.943
Non-Methyl HT-SELEX, 2 experiments	median	0.82	0.811	0.775	0.771	0.75	0.745
Non-Methyl HT-SELEX, 2 experiments	best	0.986	0.978	0.978	0.964	0.963	0.945

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	POU {3.1.10} (TFClass)
TF subfamily	HNF1-like {3.1.10.7} (TFClass)
TFClass ID	TFClass: 3.1.10.7.3
HGNC	HGNC:26137
MGI	MGI:2445066
EntrezGene (human)	GeneID:79618 (SSTAR profile)
EntrezGene (mouse)	GeneID:219150 (SSTAR profile)
UniProt ID (human)	HMBX1_HUMAN
UniProt ID (mouse)	HMBX1_MOUSE
UniProt AC (human)	Q6NT76 (TFClass)
UniProt AC (mouse)	Q8BJA3 (TFClass)
GRECO-DB-TF	no

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

PCM	HMBX1.H12INVIVO.0.PSM.A.pcm
PWM	HMBX1.H12INVIVO.0.PSM.A.pwm
PFM	HMBX1.H12INVIVO.0.PSM.A.pfm
Alignment	HMBX1.H12INVIVO.0.PSM.A.words.tsv
Threshold to P-value map	HMBX1.H12INVIVO.0.PSM.A.thr
Motif in other formats
JASPAR format	HMBX1.H12INVIVO.0.PSM.A_jaspar_format.txt
MEME format	HMBX1.H12INVIVO.0.PSM.A_meme_format.meme
Transfac format	HMBX1.H12INVIVO.0.PSM.A_transfac_format.txt
Homer format	HMBX1.H12INVIVO.0.PSM.A_homer_format_0.001.txt HMBX1.H12INVIVO.0.PSM.A_homer_format_0.0005.txt HMBX1.H12INVIVO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	376.0	108.0	353.0	163.0
02	404.0	168.0	368.0	60.0
03	36.0	695.0	42.0	227.0
04	7.0	5.0	12.0	976.0
05	644.0	3.0	352.0	1.0
06	7.0	3.0	990.0	0.0
07	3.5	6.5	18.5	971.5
08	83.5	280.5	90.5	545.5
09	878.5	7.5	52.5	61.5

PFM

	A	C	G	T
01	0.376	0.108	0.353	0.163
02	0.404	0.168	0.368	0.06
03	0.036	0.695	0.042	0.227
04	0.007	0.005	0.012	0.976
05	0.644	0.003	0.352	0.001
06	0.007	0.003	0.99	0.0
07	0.004	0.007	0.019	0.972
08	0.084	0.281	0.091	0.546
09	0.879	0.008	0.053	0.062

PWM

	A	C	G	T
01	0.406	-0.83	0.343	-0.424
02	0.477	-0.394	0.384	-1.406
03	-1.898	1.018	-1.75	-0.096
04	-3.362	-3.622	-2.909	1.357
05	0.942	-3.975	0.34	-4.525
06	-3.362	-3.975	1.371	-4.982
07	-3.875	-3.421	-2.521	1.352
08	-1.083	0.114	-1.004	0.777
09	1.252	-3.306	-1.535	-1.382

Standard thresholds

P-value	Threshold
0.001	4.974715
0.0005	5.929245
0.0001	7.50248