SHOX.H14INVIVO.1.S.D motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SHOX.H14INVIVO.1.S.D
Gene (human)	SHOX (GeneCards)
Gene synonyms (human)	PHOG
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	D

Motif length	13
Consensus	nvvbTAATTRvhh
GC content	33.48%
Information content (bits; total / per base)	12.103 / 0.931
Data sources	HT-SELEX
Aligned words	9555
Previous names	SHOX.H12INVIVO.1.S.D

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.986	0.974	0.98	0.966	0.953	0.939
Overall, 4 experiments	best	0.991	0.983	0.985	0.976	0.972	0.958
Methyl HT-SELEX, 1 experiments	median	0.989	0.98	0.984	0.973	0.972	0.958
Methyl HT-SELEX, 1 experiments	best	0.989	0.98	0.984	0.973	0.972	0.958
Non-Methyl HT-SELEX, 3 experiments	median	0.982	0.969	0.976	0.959	0.944	0.936
Non-Methyl HT-SELEX, 3 experiments	best	0.991	0.983	0.985	0.976	0.962	0.942

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.777	0.636	0.774	0.575

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
Genomic HT-SELEX	0 overall: 0 Lysate, 0 IVT, 0 GFPIVT
SMiLE-Seq	0
PBM	0

PCM	SHOX.H14INVIVO.1.S.D.pcm
PWM	SHOX.H14INVIVO.1.S.D.pwm
PFM	SHOX.H14INVIVO.1.S.D.pfm
Threshold to P-value map	SHOX.H14INVIVO.1.S.D.thr
Motif in other formats
JASPAR format	SHOX.H14INVIVO.1.S.D_jaspar_format.txt
MEME format	SHOX.H14INVIVO.1.S.D_meme_format.meme
Transfac format	SHOX.H14INVIVO.1.S.D_transfac_format.txt
Homer format	SHOX.H14INVIVO.1.S.D_homer_format_0.001.txt SHOX.H14INVIVO.1.S.D_homer_format_0.0005.txt SHOX.H14INVIVO.1.S.D_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2675.25	2248.25	2265.25	2366.25
02	2113.5	3542.5	2776.5	1122.5
03	1674.0	3905.0	3367.0	609.0
04	301.0	4813.0	2196.0	2245.0
05	0.0	0.0	0.0	9555.0
06	9555.0	0.0	0.0	0.0
07	9555.0	0.0	0.0	0.0
08	0.0	0.0	0.0	9555.0
09	0.0	32.0	28.0	9495.0
10	5497.0	60.0	3947.0	51.0
11	3806.0	1664.0	3622.0	463.0
12	2398.0	2470.0	1127.0	3560.0
13	1844.25	1830.25	1694.25	4186.25

PFM

	A	C	G	T
01	0.28	0.235	0.237	0.248
02	0.221	0.371	0.291	0.117
03	0.175	0.409	0.352	0.064
04	0.032	0.504	0.23	0.235
05	0.0	0.0	0.0	1.0
06	1.0	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	0.003	0.003	0.994
10	0.575	0.006	0.413	0.005
11	0.398	0.174	0.379	0.048
12	0.251	0.259	0.118	0.373
13	0.193	0.192	0.177	0.438

PWM

	A	C	G	T
01	0.113	-0.061	-0.053	-0.009
02	-0.122	0.394	0.15	-0.754
03	-0.355	0.491	0.343	-1.364
04	-2.065	0.7	-0.084	-0.062
05	-6.95	-6.95	-6.95	1.386
06	1.386	-6.95	-6.95	-6.95
07	1.386	-6.95	-6.95	-6.95
08	-6.95	-6.95	-6.95	1.386
09	-6.95	-4.245	-4.369	1.379
10	0.833	-3.648	0.502	-3.804
11	0.465	-0.361	0.416	-1.637
12	0.004	0.033	-0.75	0.399
13	-0.258	-0.266	-0.343	0.561

Standard thresholds

P-value	Threshold
0.001	2.039865
0.0005	4.13396
0.0001	7.95602