MSX2.H13RSNP.1.SM.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MSX2.H13RSNP.1.SM.B
Gene (human)	MSX2 (GeneCards)
Gene synonyms (human)	HOX8
Gene (mouse)	Msx2
Gene synonyms (mouse)	Hox-8.1, Msx-2
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	20
Consensus	vvbCAATTAvvnhhhAATWv
GC content	31.96%
Information content (bits; total / per base)	17.159 / 0.858
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	252
Previous names	MSX2.H12RSNP.1.SM.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.851	0.849	0.783	0.784	0.743	0.742
Overall, 4 experiments	best	0.987	0.98	0.977	0.965	0.96	0.942
Methyl HT-SELEX, 1 experiments	median	0.982	0.972	0.968	0.951	0.941	0.919
Methyl HT-SELEX, 1 experiments	best	0.982	0.972	0.968	0.951	0.941	0.919
Non-Methyl HT-SELEX, 3 experiments	median	0.721	0.725	0.598	0.616	0.544	0.565
Non-Methyl HT-SELEX, 3 experiments	best	0.987	0.98	0.977	0.965	0.96	0.942

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.601	0.046	0.556	0.373

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: 3.1.2.11.2
HGNC	HGNC:7392
MGI	MGI:97169
EntrezGene (human)	GeneID:4488 (SSTAR profile)
EntrezGene (mouse)	GeneID:17702 (SSTAR profile)
UniProt ID (human)	MSX2_HUMAN
UniProt ID (mouse)	MSX2_MOUSE
UniProt AC (human)	P35548 (TFClass)
UniProt AC (mouse)	Q03358 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	MSX2.H13RSNP.1.SM.B.pcm
PWM	MSX2.H13RSNP.1.SM.B.pwm
PFM	MSX2.H13RSNP.1.SM.B.pfm
Threshold to P-value map	MSX2.H13RSNP.1.SM.B.thr
Motif in other formats
JASPAR format	MSX2.H13RSNP.1.SM.B_jaspar_format.txt
MEME format	MSX2.H13RSNP.1.SM.B_meme_format.meme
Transfac format	MSX2.H13RSNP.1.SM.B_transfac_format.txt
Homer format	MSX2.H13RSNP.1.SM.B_homer_format_0.001.txt MSX2.H13RSNP.1.SM.B_homer_format_0.0005.txt MSX2.H13RSNP.1.SM.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	39.25	65.25	110.25	37.25
02	64.5	41.5	116.5	29.5
03	19.0	122.0	91.0	20.0
04	0.0	176.0	1.0	75.0
05	252.0	0.0	0.0	0.0
06	252.0	0.0	0.0	0.0
07	0.0	0.0	0.0	252.0
08	0.0	0.0	0.0	252.0
09	239.0	0.0	13.0	0.0
10	102.0	63.0	62.0	25.0
11	62.0	105.0	43.0	42.0
12	76.0	82.0	32.0	62.0
13	112.0	62.0	37.0	41.0
14	71.0	115.0	25.0	41.0
15	59.0	92.0	2.0	99.0
16	208.0	4.0	0.0	40.0
17	191.0	1.0	2.0	58.0
18	18.0	8.0	8.0	218.0
19	57.25	8.25	22.25	164.25
20	132.0	48.0	53.0	19.0

PFM

	A	C	G	T
01	0.156	0.259	0.438	0.148
02	0.256	0.165	0.462	0.117
03	0.075	0.484	0.361	0.079
04	0.0	0.698	0.004	0.298
05	1.0	0.0	0.0	0.0
06	1.0	0.0	0.0	0.0
07	0.0	0.0	0.0	1.0
08	0.0	0.0	0.0	1.0
09	0.948	0.0	0.052	0.0
10	0.405	0.25	0.246	0.099
11	0.246	0.417	0.171	0.167
12	0.302	0.325	0.127	0.246
13	0.444	0.246	0.147	0.163
14	0.282	0.456	0.099	0.163
15	0.234	0.365	0.008	0.393
16	0.825	0.016	0.0	0.159
17	0.758	0.004	0.008	0.23
18	0.071	0.032	0.032	0.865
19	0.227	0.033	0.088	0.652
20	0.524	0.19	0.21	0.075

PWM

	A	C	G	T
01	-0.46	0.034	0.55	-0.511
02	0.023	-0.406	0.605	-0.735
03	-1.15	0.65	0.361	-1.102
04	-3.841	1.013	-3.297	0.171
05	1.37	-3.841	-3.841	-3.841
06	1.37	-3.841	-3.841	-3.841
07	-3.841	-3.841	-3.841	1.37
08	-3.841	-3.841	-3.841	1.37
09	1.317	-3.841	-1.499	-3.841
10	0.474	0.0	-0.016	-0.892
11	-0.016	0.502	-0.372	-0.395
12	0.184	0.259	-0.657	-0.016
13	0.566	-0.016	-0.517	-0.418
14	0.117	0.592	-0.892	-0.418
15	-0.064	0.372	-2.946	0.444
16	1.179	-2.482	-3.841	-0.442
17	1.095	-3.297	-2.946	-0.081
18	-1.2	-1.926	-1.926	1.226
19	-0.094	-1.9	-1.002	0.945
20	0.728	-0.265	-0.169	-1.15

Standard thresholds

P-value	Threshold
0.001	1.94451
0.0005	3.27826
0.0001	6.06831