HMBX1.H12CORE.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	HMBX1.H12CORE.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	ndvCTAGTTAvYn
GC content	39.45%
Information content (bits; total / per base)	11.798 / 0.908
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9535

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)	0.802	0.855	0.647	0.719	0.723	0.769	2.046	2.189	82.854	128.699

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.878	0.862	0.808	0.805	0.765	0.768
Overall, 4 experiments	best	0.993	0.987	0.986	0.978	0.971	0.956
Methyl HT-SELEX, 2 experiments	median	0.88	0.866	0.809	0.808	0.765	0.768
Methyl HT-SELEX, 2 experiments	best	0.993	0.987	0.986	0.978	0.969	0.956
Non-Methyl HT-SELEX, 2 experiments	median	0.832	0.826	0.78	0.781	0.753	0.753
Non-Methyl HT-SELEX, 2 experiments	best	0.989	0.979	0.983	0.972	0.971	0.956

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.H12CORE.0.PSM.A.pcm
PWM	HMBX1.H12CORE.0.PSM.A.pwm
PFM	HMBX1.H12CORE.0.PSM.A.pfm
Alignment	HMBX1.H12CORE.0.PSM.A.words.tsv
Threshold to P-value map	HMBX1.H12CORE.0.PSM.A.thr
Motif in other formats
JASPAR format	HMBX1.H12CORE.0.PSM.A_jaspar_format.txt
MEME format	HMBX1.H12CORE.0.PSM.A_meme_format.meme
Transfac format	HMBX1.H12CORE.0.PSM.A_transfac_format.txt
Homer format	HMBX1.H12CORE.0.PSM.A_homer_format_0.001.txt HMBX1.H12CORE.0.PSM.A_homer_format_0.0005.txt HMBX1.H12CORE.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2360.0	2073.0	1747.0	3355.0
02	4502.0	1356.0	1903.0	1774.0
03	4113.0	2048.0	2821.0	553.0
04	412.0	7382.0	133.0	1608.0
05	219.0	233.0	130.0	8953.0
06	6702.0	0.0	2833.0	0.0
07	0.0	0.0	9535.0	0.0
08	0.0	0.0	0.0	9535.0
09	684.0	477.0	167.0	8207.0
10	9339.0	4.0	191.0	1.0
11	3213.0	3328.0	1798.0	1196.0
12	442.0	5291.0	1112.0	2690.0
13	2763.25	1960.25	2376.25	2435.25

PFM

	A	C	G	T
01	0.248	0.217	0.183	0.352
02	0.472	0.142	0.2	0.186
03	0.431	0.215	0.296	0.058
04	0.043	0.774	0.014	0.169
05	0.023	0.024	0.014	0.939
06	0.703	0.0	0.297	0.0
07	0.0	0.0	1.0	0.0
08	0.0	0.0	0.0	1.0
09	0.072	0.05	0.018	0.861
10	0.979	0.0	0.02	0.0
11	0.337	0.349	0.189	0.125
12	0.046	0.555	0.117	0.282
13	0.29	0.206	0.249	0.255

PWM

	A	C	G	T
01	-0.01	-0.14	-0.31	0.341
02	0.635	-0.563	-0.225	-0.295
03	0.545	-0.152	0.168	-1.458
04	-1.751	1.13	-2.87	-0.393
05	-2.378	-2.317	-2.892	1.323
06	1.033	-6.949	0.173	-6.949
07	-6.949	-6.949	1.386	-6.949
08	-6.949	-6.949	-6.949	1.386
09	-1.246	-1.605	-2.646	1.236
10	1.365	-5.938	-2.513	-6.586
11	0.298	0.333	-0.282	-0.689
12	-1.681	0.797	-0.761	0.121
13	0.148	-0.195	-0.003	0.021

Standard thresholds

P-value	Threshold
0.001	4.03381
0.0005	5.23221
0.0001	7.45171