MSX1.H12INVIVO.0.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MSX1.H12INVIVO.0.SM.D
Gene (human)	MSX1 (GeneCards)
Gene synonyms (human)	HOX7
Gene (mouse)	Msx1
Gene synonyms (mouse)	Hox7, Hox7.1
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	11
Consensus	nvYAATTAvbn
GC content	33.79%
Information content (bits; total / per base)	11.505 / 1.046
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	8860

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.869	0.821	0.74	0.718	0.633	0.638
Overall, 8 experiments	best	0.982	0.973	0.935	0.919	0.847	0.823
Methyl HT-SELEX, 2 experiments	median	0.898	0.862	0.822	0.797	0.728	0.72
Methyl HT-SELEX, 2 experiments	best	0.957	0.929	0.935	0.902	0.847	0.823
Non-Methyl HT-SELEX, 6 experiments	median	0.869	0.821	0.74	0.718	0.633	0.638
Non-Methyl HT-SELEX, 6 experiments	best	0.982	0.973	0.933	0.919	0.843	0.82

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.855	0.57	0.791	0.594

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	NK-related {3.1.2} (TFClass)
TF subfamily	MSX {3.1.2.11} (TFClass)
TFClass ID	TFClass: 3.1.2.11.1
HGNC	HGNC:7391
MGI	MGI:97168
EntrezGene (human)	GeneID:4487 (SSTAR profile)
EntrezGene (mouse)	GeneID:17701 (SSTAR profile)
UniProt ID (human)	MSX1_HUMAN
UniProt ID (mouse)	MSX1_MOUSE
UniProt AC (human)	P28360 (TFClass)
UniProt AC (mouse)	P13297 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	MSX1.H12INVIVO.0.SM.D.pcm
PWM	MSX1.H12INVIVO.0.SM.D.pwm
PFM	MSX1.H12INVIVO.0.SM.D.pfm
Alignment	MSX1.H12INVIVO.0.SM.D.words.tsv
Threshold to P-value map	MSX1.H12INVIVO.0.SM.D.thr
Motif in other formats
JASPAR format	MSX1.H12INVIVO.0.SM.D_jaspar_format.txt
MEME format	MSX1.H12INVIVO.0.SM.D_meme_format.meme
Transfac format	MSX1.H12INVIVO.0.SM.D_transfac_format.txt
Homer format	MSX1.H12INVIVO.0.SM.D_homer_format_0.001.txt MSX1.H12INVIVO.0.SM.D_homer_format_0.0005.txt MSX1.H12INVIVO.0.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2484.25	2446.25	2044.25	1885.25
02	1186.25	3256.25	3240.25	1177.25
03	44.0	5159.0	8.0	3649.0
04	8858.0	2.0	0.0	0.0
05	8860.0	0.0	0.0	0.0
06	0.0	0.0	0.0	8860.0
07	0.0	0.0	0.0	8860.0
08	8854.0	0.0	6.0	0.0
09	2583.0	2498.0	3038.0	741.0
10	744.5	4151.5	2208.5	1755.5
11	2012.25	2289.25	2581.25	1977.25

PFM

	A	C	G	T
01	0.28	0.276	0.231	0.213
02	0.134	0.368	0.366	0.133
03	0.005	0.582	0.001	0.412
04	1.0	0.0	0.0	0.0
05	1.0	0.0	0.0	0.0
06	0.0	0.0	0.0	1.0
07	0.0	0.0	0.0	1.0
08	0.999	0.0	0.001	0.0
09	0.292	0.282	0.343	0.084
10	0.084	0.469	0.249	0.198
11	0.227	0.258	0.291	0.223

PWM

	A	C	G	T
01	0.115	0.099	-0.08	-0.161
02	-0.624	0.385	0.38	-0.631
03	-3.869	0.845	-5.375	0.499
04	1.385	-6.252	-6.883	-6.883
05	1.386	-6.883	-6.883	-6.883
06	-6.883	-6.883	-6.883	1.386
07	-6.883	-6.883	-6.883	1.386
08	1.385	-6.883	-5.591	-6.883
09	0.154	0.12	0.316	-1.093
10	-1.088	0.628	-0.003	-0.232
11	-0.096	0.033	0.153	-0.113

Standard thresholds

P-value	Threshold
0.001	1.04991
0.0005	4.21101
0.0001	8.04351