MSX1.H12RSNP.1.S.C motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MSX1.H12RSNP.1.S.C
Gene (human)	MSX1 (GeneCards)
Gene synonyms (human)	HOX7
Gene (mouse)	Msx1
Gene synonyms (mouse)	Hox7, Hox7.1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	C

Motif length	22
Consensus	nnvbCAATTAvnnnbhAATTWn
GC content	31.04%
Information content (bits; total / per base)	17.53 / 0.797
Data sources	HT-SELEX
Aligned words	4727

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.869	0.836	0.729	0.718	0.622	0.634
Overall, 8 experiments	best	0.995	0.993	0.934	0.93	0.812	0.783
Methyl HT-SELEX, 2 experiments	median	0.886	0.848	0.798	0.773	0.704	0.697
Methyl HT-SELEX, 2 experiments	best	0.935	0.895	0.902	0.858	0.81	0.782
Non-Methyl HT-SELEX, 6 experiments	median	0.869	0.836	0.729	0.718	0.622	0.634
Non-Methyl HT-SELEX, 6 experiments	best	0.995	0.993	0.934	0.93	0.812	0.783

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.765	0.441	0.734	0.561

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.H12RSNP.1.S.C.pcm
PWM	MSX1.H12RSNP.1.S.C.pwm
PFM	MSX1.H12RSNP.1.S.C.pfm
Alignment	MSX1.H12RSNP.1.S.C.words.tsv
Threshold to P-value map	MSX1.H12RSNP.1.S.C.thr
Motif in other formats
JASPAR format	MSX1.H12RSNP.1.S.C_jaspar_format.txt
MEME format	MSX1.H12RSNP.1.S.C_meme_format.meme
Transfac format	MSX1.H12RSNP.1.S.C_transfac_format.txt
Homer format	MSX1.H12RSNP.1.S.C_homer_format_0.001.txt MSX1.H12RSNP.1.S.C_homer_format_0.0005.txt MSX1.H12RSNP.1.S.C_homer_format_0.0001.txt

PCM

	A	C	G	T
01	1625.75	762.75	1065.75	1272.75
02	1415.5	1055.5	1565.5	690.5
03	2022.0	820.0	1297.0	588.0
04	382.0	2165.0	1745.0	435.0
05	4.0	3111.0	7.0	1605.0
06	4713.0	5.0	9.0	0.0
07	4727.0	0.0	0.0	0.0
08	0.0	0.0	0.0	4727.0
09	0.0	8.0	0.0	4719.0
10	4591.0	0.0	134.0	2.0
11	1933.0	801.0	1615.0	378.0
12	1248.0	1549.0	934.0	996.0
13	1524.0	818.0	1217.0	1168.0
14	1807.0	1089.0	880.0	951.0
15	784.0	1950.0	1147.0	846.0
16	657.0	2355.0	180.0	1535.0
17	3833.0	273.0	211.0	410.0
18	3830.0	155.0	85.0	657.0
19	447.0	105.0	68.0	4107.0
20	721.0	127.0	139.0	3740.0
21	3527.0	187.0	468.0	545.0
22	1565.75	954.75	1224.75	981.75

PFM

	A	C	G	T
01	0.344	0.161	0.225	0.269
02	0.299	0.223	0.331	0.146
03	0.428	0.173	0.274	0.124
04	0.081	0.458	0.369	0.092
05	0.001	0.658	0.001	0.34
06	0.997	0.001	0.002	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.002	0.0	0.998
10	0.971	0.0	0.028	0.0
11	0.409	0.169	0.342	0.08
12	0.264	0.328	0.198	0.211
13	0.322	0.173	0.257	0.247
14	0.382	0.23	0.186	0.201
15	0.166	0.413	0.243	0.179
16	0.139	0.498	0.038	0.325
17	0.811	0.058	0.045	0.087
18	0.81	0.033	0.018	0.139
19	0.095	0.022	0.014	0.869
20	0.153	0.027	0.029	0.791
21	0.746	0.04	0.099	0.115
22	0.331	0.202	0.259	0.208

PWM

	A	C	G	T
01	0.318	-0.437	-0.103	0.074
02	0.18	-0.113	0.281	-0.536
03	0.536	-0.365	0.093	-0.696
04	-1.126	0.605	0.389	-0.996
05	-5.266	0.967	-4.867	0.306
06	1.382	-5.114	-4.668	-6.327
07	1.385	-6.327	-6.327	-6.327
08	-6.327	-6.327	-6.327	1.385
09	-6.327	-4.762	-6.327	1.383
10	1.356	-6.327	-2.163	-5.662
11	0.491	-0.388	0.312	-1.136
12	0.054	0.27	-0.235	-0.171
13	0.254	-0.367	0.029	-0.012
14	0.424	-0.082	-0.294	-0.217
15	-0.409	0.5	-0.03	-0.334
16	-0.586	0.689	-1.872	0.261
17	1.175	-1.459	-1.715	-1.055
18	1.175	-2.02	-2.609	-0.586
19	-0.969	-2.403	-2.826	1.244
20	-0.493	-2.216	-2.127	1.151
21	1.092	-1.834	-0.924	-0.772
22	0.281	-0.213	0.036	-0.185

Standard thresholds

P-value	Threshold
0.001	0.05931
0.0005	1.75236
0.0001	5.27306