SPDEF.H12RSNP.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SPDEF.H12RSNP.0.PSM.A
Gene (human)	SPDEF (GeneCards)
Gene synonyms (human)	PDEF, PSE
Gene (mouse)	Spdef
Gene synonyms (mouse)	Pdef, Pse
LOGO
LOGO (reverse complement)
Motif subtype	0
Quality	A

Motif length	12
Consensus	nWvCCGGATRYn
GC content	54.65%
Information content (bits; total / per base)	14.389 / 1.199
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9421

ChIP-Seq benchmarking	Num. of experiments (peaksets)	auROC, median	auROC, best	auPRC, median	auPRC, best	pseudo-auROC, median	pseudo-auROC, best	pseudo-log-auROC, median	pseudo-log-auROC, best	Centrality, median	Centrality, best
Human	2 (12)	0.829	0.899	0.762	0.83	0.768	0.847	2.494	2.865	63.057	144.77

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.806	0.795	0.65	0.664	0.573	0.595
Overall, 8 experiments	best	0.998	0.996	0.995	0.992	0.961	0.957
Methyl HT-SELEX, 2 experiments	median	0.841	0.837	0.763	0.768	0.672	0.688
Methyl HT-SELEX, 2 experiments	best	0.983	0.974	0.954	0.938	0.823	0.826
Non-Methyl HT-SELEX, 6 experiments	median	0.806	0.795	0.65	0.664	0.573	0.595
Non-Methyl HT-SELEX, 6 experiments	best	0.998	0.996	0.995	0.992	0.961	0.957

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.752	0.617	0.75	0.526

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Tryptophan cluster factors {3.5} (TFClass)
TF family	Ets-related {3.5.2} (TFClass)
TF subfamily	SPDEF-like {3.5.2.7} (TFClass)
TFClass ID	TFClass: 3.5.2.7.1
HGNC	HGNC:17257
MGI	MGI:1353422
EntrezGene (human)	GeneID:25803 (SSTAR profile)
EntrezGene (mouse)	GeneID:30051 (SSTAR profile)
UniProt ID (human)	SPDEF_HUMAN
UniProt ID (mouse)	SPDEF_MOUSE
UniProt AC (human)	O95238 (TFClass)
UniProt AC (mouse)	Q9WTP3 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	2 human, 0 mouse
HT-SELEX	6
Methyl-HT-SELEX	2

PCM	SPDEF.H12RSNP.0.PSM.A.pcm
PWM	SPDEF.H12RSNP.0.PSM.A.pwm
PFM	SPDEF.H12RSNP.0.PSM.A.pfm
Alignment	SPDEF.H12RSNP.0.PSM.A.words.tsv
Threshold to P-value map	SPDEF.H12RSNP.0.PSM.A.thr
Motif in other formats
JASPAR format	SPDEF.H12RSNP.0.PSM.A_jaspar_format.txt
MEME format	SPDEF.H12RSNP.0.PSM.A_meme_format.meme
Transfac format	SPDEF.H12RSNP.0.PSM.A_transfac_format.txt
Homer format	SPDEF.H12RSNP.0.PSM.A_homer_format_0.001.txt SPDEF.H12RSNP.0.PSM.A_homer_format_0.0005.txt SPDEF.H12RSNP.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2762.5	1875.5	2706.5	2076.5
02	6431.25	221.25	379.25	2389.25
03	3974.0	3185.0	1338.0	924.0
04	23.0	9270.0	127.0	1.0
05	35.0	9385.0	0.0	1.0
06	0.0	0.0	9421.0	0.0
07	0.0	0.0	9421.0	0.0
08	9421.0	0.0	0.0	0.0
09	379.0	7.0	0.0	9035.0
10	2268.0	694.0	6381.0	78.0
11	157.5	2869.5	89.5	6304.5
12	2918.5	1549.5	2865.5	2087.5

PFM

	A	C	G	T
01	0.293	0.199	0.287	0.22
02	0.683	0.023	0.04	0.254
03	0.422	0.338	0.142	0.098
04	0.002	0.984	0.013	0.0
05	0.004	0.996	0.0	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	1.0	0.0	0.0	0.0
09	0.04	0.001	0.0	0.959
10	0.241	0.074	0.677	0.008
11	0.017	0.305	0.01	0.669
12	0.31	0.164	0.304	0.222

PWM

	A	C	G	T
01	0.159	-0.228	0.139	-0.126
02	1.004	-2.356	-1.821	0.014
03	0.523	0.302	-0.565	-0.934
04	-4.535	1.369	-2.903	-6.575
05	-4.147	1.382	-6.938	-6.575
06	-6.938	-6.938	1.386	-6.938
07	-6.938	-6.938	1.386	-6.938
08	1.386	-6.938	-6.938	-6.938
09	-1.822	-5.537	-6.938	1.344
10	-0.038	-1.22	0.996	-3.38
11	-2.692	0.197	-3.246	0.984
12	0.214	-0.418	0.196	-0.121

Standard thresholds

P-value	Threshold
0.001	1.0545
0.0005	2.698865
0.0001	6.519905