HMBX1.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HMBX1.H12INVITRO.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	13
Consensus	ndvCTAGTWAMYd
GC content	40.28%
Information content (bits; total / per base)	12.678 / 0.975
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	2470

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)	0.789	0.836	0.636	0.696	0.702	0.743	1.898	2.023	73.921	111.886

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.882	0.87	0.811	0.809	0.765	0.769
Overall, 4 experiments	best	0.992	0.987	0.986	0.978	0.972	0.959
Methyl HT-SELEX, 2 experiments	median	0.882	0.872	0.811	0.811	0.765	0.769
Methyl HT-SELEX, 2 experiments	best	0.992	0.987	0.986	0.978	0.968	0.955
Non-Methyl HT-SELEX, 2 experiments	median	0.834	0.832	0.782	0.785	0.755	0.756
Non-Methyl HT-SELEX, 2 experiments	best	0.991	0.984	0.985	0.976	0.972	0.959

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.H12INVITRO.0.PSM.A.pcm
PWM	HMBX1.H12INVITRO.0.PSM.A.pwm
PFM	HMBX1.H12INVITRO.0.PSM.A.pfm
Alignment	HMBX1.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	HMBX1.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	HMBX1.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	HMBX1.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	HMBX1.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	HMBX1.H12INVITRO.0.PSM.A_homer_format_0.001.txt HMBX1.H12INVITRO.0.PSM.A_homer_format_0.0005.txt HMBX1.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	652.25	583.25	410.25	824.25
02	1372.0	359.0	378.0	361.0
03	1008.0	990.0	385.0	87.0
04	45.0	2203.0	26.0	196.0
05	103.0	0.0	32.0	2335.0
06	1988.0	50.0	432.0	0.0
07	0.0	5.0	2465.0	0.0
08	1.0	3.0	1.0	2465.0
09	603.0	120.0	69.0	1678.0
10	2425.0	24.0	15.0	6.0
11	322.0	1722.0	232.0	194.0
12	113.25	1327.25	300.25	729.25
13	972.25	376.25	426.25	695.25

PFM

	A	C	G	T
01	0.264	0.236	0.166	0.334
02	0.555	0.145	0.153	0.146
03	0.408	0.401	0.156	0.035
04	0.018	0.892	0.011	0.079
05	0.042	0.0	0.013	0.945
06	0.805	0.02	0.175	0.0
07	0.0	0.002	0.998	0.0
08	0.0	0.001	0.0	0.998
09	0.244	0.049	0.028	0.679
10	0.982	0.01	0.006	0.002
11	0.13	0.697	0.094	0.079
12	0.046	0.537	0.122	0.295
13	0.394	0.152	0.173	0.281

PWM

	A	C	G	T
01	0.055	-0.057	-0.407	0.288
02	0.797	-0.54	-0.489	-0.535
03	0.489	0.471	-0.471	-1.941
04	-2.58	1.27	-3.098	-1.141
05	-1.775	-5.759	-2.904	1.328
06	1.167	-2.478	-0.356	-5.759
07	-5.759	-4.49	1.382	-5.759
08	-5.346	-4.829	-5.346	1.382
09	-0.024	-1.625	-2.167	0.998
10	1.366	-3.173	-3.598	-4.355
11	-0.648	1.024	-0.974	-1.151
12	-1.682	0.763	-0.718	0.166
13	0.453	-0.493	-0.369	0.118

Standard thresholds

P-value	Threshold
0.001	3.66256
0.0005	4.86351
0.0001	7.238765