SHOX.H13RSNP.1.S.B motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SHOX.H13RSNP.1.S.B
Gene (human)	SHOX (GeneCards)
Gene synonyms (human)	PHOG
Gene (mouse)
Gene synonyms (mouse)
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	B

Motif length	13
Consensus	nnnnYTAATTRvn
GC content	29.71%
Information content (bits; total / per base)	11.655 / 0.897
Data sources	HT-SELEX
Aligned words	9486
Previous names	SHOX.H12RSNP.1.S.B

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.977	0.961	0.971	0.952	0.947	0.927
Overall, 4 experiments	best	0.987	0.978	0.981	0.969	0.967	0.948
Methyl HT-SELEX, 1 experiments	median	0.983	0.971	0.978	0.962	0.967	0.948
Methyl HT-SELEX, 1 experiments	best	0.983	0.971	0.978	0.962	0.967	0.948
Non-Methyl HT-SELEX, 3 experiments	median	0.972	0.952	0.965	0.941	0.939	0.926
Non-Methyl HT-SELEX, 3 experiments	best	0.987	0.978	0.981	0.969	0.954	0.928

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.787	0.653	0.753	0.553

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.H13RSNP.1.S.B.pcm
PWM	SHOX.H13RSNP.1.S.B.pwm
PFM	SHOX.H13RSNP.1.S.B.pfm
Threshold to P-value map	SHOX.H13RSNP.1.S.B.thr
Motif in other formats
JASPAR format	SHOX.H13RSNP.1.S.B_jaspar_format.txt
MEME format	SHOX.H13RSNP.1.S.B_meme_format.meme
Transfac format	SHOX.H13RSNP.1.S.B_transfac_format.txt
Homer format	SHOX.H13RSNP.1.S.B_homer_format_0.001.txt SHOX.H13RSNP.1.S.B_homer_format_0.0005.txt SHOX.H13RSNP.1.S.B_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2205.0	1907.0	1858.0	3516.0
02	1868.25	2299.25	2200.25	3118.25
03	2109.0	3015.0	2525.0	1837.0
04	2576.0	2466.0	3214.0	1230.0
05	168.0	3858.0	1138.0	4322.0
06	0.0	69.0	1.0	9416.0
07	9486.0	0.0	0.0	0.0
08	9486.0	0.0	0.0	0.0
09	0.0	0.0	0.0	9486.0
10	0.0	15.0	20.0	9451.0
11	6342.0	51.0	3028.0	65.0
12	3186.75	1795.75	3102.75	1400.75
13	2578.0	2011.0	2058.0	2839.0

PFM

	A	C	G	T
01	0.232	0.201	0.196	0.371
02	0.197	0.242	0.232	0.329
03	0.222	0.318	0.266	0.194
04	0.272	0.26	0.339	0.13
05	0.018	0.407	0.12	0.456
06	0.0	0.007	0.0	0.993
07	1.0	0.0	0.0	0.0
08	1.0	0.0	0.0	0.0
09	0.0	0.0	0.0	1.0
10	0.0	0.002	0.002	0.996
11	0.669	0.005	0.319	0.007
12	0.336	0.189	0.327	0.148
13	0.272	0.212	0.217	0.299

PWM

	A	C	G	T
01	-0.073	-0.218	-0.244	0.393
02	-0.238	-0.031	-0.075	0.274
03	-0.117	0.24	0.063	-0.255
04	0.083	0.039	0.304	-0.656
05	-2.635	0.486	-0.733	0.6
06	-6.944	-3.505	-6.582	1.378
07	1.386	-6.944	-6.944	-6.944
08	1.386	-6.944	-6.944	-6.944
09	-6.944	-6.944	-6.944	1.386
10	-6.944	-4.922	-4.668	1.382
11	0.983	-3.797	0.244	-3.563
12	0.295	-0.278	0.269	-0.526
13	0.083	-0.165	-0.142	0.18

Standard thresholds

P-value	Threshold
0.001	2.60936
0.0005	4.26132
0.0001	8.07694