MSX2.H12INVIVO.1.SM.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MSX2.H12INVIVO.1.SM.D
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	D

Motif length	20
Consensus	bhhWWddnnnSTAATTASbv
GC content	34.61%
Information content (bits; total / per base)	14.269 / 0.713
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	556

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.868	0.863	0.795	0.796	0.755	0.756
Overall, 4 experiments	best	0.989	0.982	0.982	0.971	0.971	0.956
Methyl HT-SELEX, 1 experiments	median	0.984	0.974	0.973	0.958	0.957	0.937
Methyl HT-SELEX, 1 experiments	best	0.984	0.974	0.973	0.958	0.957	0.937
Non-Methyl HT-SELEX, 3 experiments	median	0.752	0.751	0.617	0.633	0.553	0.576
Non-Methyl HT-SELEX, 3 experiments	best	0.989	0.982	0.982	0.971	0.971	0.956

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.584	0.051	0.427	0.264

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

PCM	MSX2.H12INVIVO.1.SM.D.pcm
PWM	MSX2.H12INVIVO.1.SM.D.pwm
PFM	MSX2.H12INVIVO.1.SM.D.pfm
Alignment	MSX2.H12INVIVO.1.SM.D.words.tsv
Threshold to P-value map	MSX2.H12INVIVO.1.SM.D.thr
Motif in other formats
JASPAR format	MSX2.H12INVIVO.1.SM.D_jaspar_format.txt
MEME format	MSX2.H12INVIVO.1.SM.D_meme_format.meme
Transfac format	MSX2.H12INVIVO.1.SM.D_transfac_format.txt
Homer format	MSX2.H12INVIVO.1.SM.D_homer_format_0.001.txt MSX2.H12INVIVO.1.SM.D_homer_format_0.0005.txt MSX2.H12INVIVO.1.SM.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	90.0	241.0	106.0	119.0
02	304.5	117.5	52.5	81.5
03	355.0	73.0	55.0	73.0
04	148.0	46.0	32.0	330.0
05	118.0	40.0	37.0	361.0
06	301.0	47.0	70.0	138.0
07	213.0	86.0	109.0	148.0
08	156.0	112.0	115.0	173.0
09	187.0	133.0	110.0	126.0
10	162.0	128.0	189.0	77.0
11	39.0	328.0	108.0	81.0
12	0.0	208.0	0.0	348.0
13	556.0	0.0	0.0	0.0
14	556.0	0.0	0.0	0.0
15	0.0	0.0	0.0	556.0
16	0.0	0.0	0.0	556.0
17	491.0	0.0	65.0	0.0
18	63.0	167.0	303.0	23.0
19	52.0	226.0	169.0	109.0
20	95.25	143.25	232.25	85.25

PFM

	A	C	G	T
01	0.162	0.433	0.191	0.214
02	0.548	0.211	0.094	0.147
03	0.638	0.131	0.099	0.131
04	0.266	0.083	0.058	0.594
05	0.212	0.072	0.067	0.649
06	0.541	0.085	0.126	0.248
07	0.383	0.155	0.196	0.266
08	0.281	0.201	0.207	0.311
09	0.336	0.239	0.198	0.227
10	0.291	0.23	0.34	0.138
11	0.07	0.59	0.194	0.146
12	0.0	0.374	0.0	0.626
13	1.0	0.0	0.0	0.0
14	1.0	0.0	0.0	0.0
15	0.0	0.0	0.0	1.0
16	0.0	0.0	0.0	1.0
17	0.883	0.0	0.117	0.0
18	0.113	0.3	0.545	0.041
19	0.094	0.406	0.304	0.196
20	0.171	0.258	0.418	0.153

PWM

	A	C	G	T
01	-0.429	0.546	-0.268	-0.153
02	0.778	-0.166	-0.955	-0.526
03	0.931	-0.634	-0.91	-0.634
04	0.062	-1.083	-1.432	0.858
05	-0.162	-1.218	-1.293	0.947
06	0.767	-1.063	-0.675	-0.007
07	0.423	-0.473	-0.24	0.062
08	0.114	-0.213	-0.187	0.217
09	0.294	-0.044	-0.231	-0.097
10	0.152	-0.081	0.304	-0.582
11	-1.242	0.852	-0.249	-0.532
12	-4.488	0.399	-4.488	0.911
13	1.378	-4.488	-4.488	-4.488
14	1.378	-4.488	-4.488	-4.488
15	-4.488	-4.488	-4.488	1.378
16	-4.488	-4.488	-4.488	1.378
17	1.254	-4.488	-0.747	-4.488
18	-0.778	0.182	0.773	-1.744
19	-0.965	0.482	0.193	-0.24
20	-0.373	0.03	0.509	-0.482

Standard thresholds

P-value	Threshold
0.001	2.88096
0.0005	4.24216
0.0001	7.01061