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

Motif	SHOX.H12INVIVO.0.SM.D
Gene (human)	SHOX (GeneCards)
Gene synonyms (human)	PHOG
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	D

Motif length	19
Consensus	nnvbTAATTARnbdddddn
GC content	33.24%
Information content (bits; total / per base)	13.383 / 0.704
Data sources	HT-SELEX + Methyl-HT-SELEX
Aligned words	9887

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.991	0.986	0.984	0.975	0.953	0.942
Overall, 4 experiments	best	0.995	0.993	0.989	0.983	0.976	0.966
Methyl HT-SELEX, 1 experiments	median	0.995	0.992	0.989	0.983	0.976	0.966
Methyl HT-SELEX, 1 experiments	best	0.995	0.992	0.989	0.983	0.976	0.966
Non-Methyl HT-SELEX, 3 experiments	median	0.988	0.98	0.98	0.968	0.94	0.936
Non-Methyl HT-SELEX, 3 experiments	best	0.995	0.993	0.988	0.983	0.966	0.949

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.772	0.619	0.707	0.545

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	Paired-related HD {3.1.3} (TFClass)
TF subfamily	SHOX {3.1.3.25} (TFClass)
TFClass ID	TFClass: 3.1.3.25.1
HGNC	HGNC:10853
MGI
EntrezGene (human)	GeneID:6473 (SSTAR profile)
EntrezGene (mouse)
UniProt ID (human)	SHOX_HUMAN
UniProt ID (mouse)
UniProt AC (human)	O15266 (TFClass)
UniProt AC (mouse)
GRECO-DB-TF	yes

ChIP-Seq	0 human, 0 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

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

PCM

	A	C	G	T
01	2216.5	2350.5	3076.5	2243.5
02	1641.25	3611.25	2864.25	1770.25
03	1958.0	2723.0	4550.0	656.0
04	505.0	4924.0	1982.0	2476.0
05	7.0	121.0	1.0	9758.0
06	9881.0	2.0	4.0	0.0
07	9887.0	0.0	0.0	0.0
08	0.0	1.0	0.0	9886.0
09	1.0	11.0	29.0	9846.0
10	6255.0	19.0	3583.0	30.0
11	3636.0	1349.0	4790.0	112.0
12	2312.0	2461.0	2019.0	3095.0
13	883.0	2028.0	1564.0	5412.0
14	3393.0	1511.0	1546.0	3437.0
15	5888.0	1050.0	1346.0	1603.0
16	3323.0	1136.0	1600.0	3828.0
17	2216.0	1348.0	1457.0	4866.0
18	3303.75	989.75	2252.75	3340.75
19	3111.0	1568.0	2573.0	2635.0

PFM

	A	C	G	T
01	0.224	0.238	0.311	0.227
02	0.166	0.365	0.29	0.179
03	0.198	0.275	0.46	0.066
04	0.051	0.498	0.2	0.25
05	0.001	0.012	0.0	0.987
06	0.999	0.0	0.0	0.0
07	1.0	0.0	0.0	0.0
08	0.0	0.0	0.0	1.0
09	0.0	0.001	0.003	0.996
10	0.633	0.002	0.362	0.003
11	0.368	0.136	0.484	0.011
12	0.234	0.249	0.204	0.313
13	0.089	0.205	0.158	0.547
14	0.343	0.153	0.156	0.348
15	0.596	0.106	0.136	0.162
16	0.336	0.115	0.162	0.387
17	0.224	0.136	0.147	0.492
18	0.334	0.1	0.228	0.338
19	0.315	0.159	0.26	0.267

PWM

	A	C	G	T
01	-0.109	-0.05	0.219	-0.097
02	-0.409	0.379	0.147	-0.333
03	-0.233	0.097	0.61	-1.324
04	-1.585	0.689	-0.221	0.002
05	-5.584	-2.999	-6.62	1.372
06	1.385	-6.355	-5.973	-6.981
07	1.386	-6.981	-6.981	-6.981
08	-6.981	-6.62	-6.981	1.385
09	-6.62	-5.226	-4.37	1.381
10	0.928	-4.755	0.371	-4.339
11	0.386	-0.605	0.661	-3.075
12	-0.067	-0.004	-0.202	0.225
13	-1.028	-0.198	-0.457	0.783
14	0.317	-0.492	-0.469	0.329
15	0.867	-0.855	-0.607	-0.433
16	0.296	-0.776	-0.434	0.437
17	-0.109	-0.606	-0.528	0.677
18	0.29	-0.914	-0.093	0.301
19	0.23	-0.455	0.04	0.064

Standard thresholds

P-value	Threshold
0.001	1.87816
0.0005	3.61391
0.0001	7.36391