MSX1.H12INVIVO.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	MSX1.H12INVIVO.1.S.D
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	D

Motif length	22
Consensus	nnvbYAATTAvnnnnhWWWWdn
GC content	31.32%
Information content (bits; total / per base)	14.17 / 0.644
Data sources	HT-SELEX
Aligned words	8743

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.874	0.84	0.734	0.722	0.625	0.637
Overall, 8 experiments	best	0.994	0.992	0.936	0.932	0.825	0.797
Methyl HT-SELEX, 2 experiments	median	0.892	0.854	0.808	0.782	0.712	0.706
Methyl HT-SELEX, 2 experiments	best	0.939	0.897	0.915	0.872	0.823	0.795
Non-Methyl HT-SELEX, 6 experiments	median	0.874	0.84	0.734	0.722	0.625	0.637
Non-Methyl HT-SELEX, 6 experiments	best	0.994	0.992	0.936	0.932	0.825	0.797

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.735	0.435	0.705	0.532

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.1.S.D.pcm
PWM	MSX1.H12INVIVO.1.S.D.pwm
PFM	MSX1.H12INVIVO.1.S.D.pfm
Alignment	MSX1.H12INVIVO.1.S.D.words.tsv
Threshold to P-value map	MSX1.H12INVIVO.1.S.D.thr
Motif in other formats
JASPAR format	MSX1.H12INVIVO.1.S.D_jaspar_format.txt
MEME format	MSX1.H12INVIVO.1.S.D_meme_format.meme
Transfac format	MSX1.H12INVIVO.1.S.D_transfac_format.txt
Homer format	MSX1.H12INVIVO.1.S.D_homer_format_0.001.txt MSX1.H12INVIVO.1.S.D_homer_format_0.0005.txt MSX1.H12INVIVO.1.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2926.75	1427.75	1898.75	2489.75
02	2674.5	1911.5	2712.5	1444.5
03	3533.0	1613.0	2349.0	1248.0
04	841.0	3733.0	3138.0	1031.0
05	14.0	5179.0	19.0	3531.0
06	8699.0	17.0	26.0	1.0
07	8742.0	0.0	1.0	0.0
08	0.0	0.0	0.0	8743.0
09	0.0	22.0	1.0	8720.0
10	8411.0	2.0	325.0	5.0
11	3310.0	1628.0	3004.0	801.0
12	1973.0	2887.0	1856.0	2027.0
13	2556.0	1716.0	2188.0	2283.0
14	3125.0	2124.0	1693.0	1801.0
15	2026.0	2903.0	1805.0	2009.0
16	2075.0	3169.0	742.0	2757.0
17	5329.0	976.0	705.0	1733.0
18	5401.0	625.0	482.0	2235.0
19	2045.0	508.0	471.0	5719.0
20	2412.0	552.0	580.0	5199.0
21	4851.5	708.5	1012.5	2170.5
22	2890.0	1589.0	1950.0	2314.0

PFM

	A	C	G	T
01	0.335	0.163	0.217	0.285
02	0.306	0.219	0.31	0.165
03	0.404	0.184	0.269	0.143
04	0.096	0.427	0.359	0.118
05	0.002	0.592	0.002	0.404
06	0.995	0.002	0.003	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.003	0.0	0.997
10	0.962	0.0	0.037	0.001
11	0.379	0.186	0.344	0.092
12	0.226	0.33	0.212	0.232
13	0.292	0.196	0.25	0.261
14	0.357	0.243	0.194	0.206
15	0.232	0.332	0.206	0.23
16	0.237	0.362	0.085	0.315
17	0.61	0.112	0.081	0.198
18	0.618	0.071	0.055	0.256
19	0.234	0.058	0.054	0.654
20	0.276	0.063	0.066	0.595
21	0.555	0.081	0.116	0.248
22	0.331	0.182	0.223	0.265

PWM

	A	C	G	T
01	0.292	-0.425	-0.141	0.13
02	0.202	-0.134	0.216	-0.414
03	0.48	-0.303	0.072	-0.56
04	-0.953	0.535	0.361	-0.75
05	-4.901	0.862	-4.634	0.479
06	1.38	-4.732	-4.349	-6.506
07	1.385	-6.871	-6.506	-6.871
08	-6.871	-6.871	-6.871	1.386
09	-6.871	-4.502	-6.506	1.383
10	1.347	-6.239	-1.9	-5.707
11	0.415	-0.294	0.318	-1.002
12	-0.102	0.278	-0.163	-0.075
13	0.156	-0.242	0.001	0.043
14	0.357	-0.029	-0.255	-0.193
15	-0.076	0.284	-0.191	-0.084
16	-0.052	0.371	-1.078	0.232
17	0.891	-0.805	-1.129	-0.232
18	0.904	-1.249	-1.508	0.022
19	-0.066	-1.456	-1.531	0.961
20	0.098	-1.373	-1.324	0.866
21	0.797	-1.124	-0.768	-0.007
22	0.279	-0.318	-0.114	0.057

Standard thresholds

P-value	Threshold
0.001	1.89971
0.0005	3.62356
0.0001	6.94061