SPDEF.H12INVITRO.0.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	SPDEF.H12INVITRO.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	55.35%
Information content (bits; total / per base)	12.53 / 1.044
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9941

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)	0.833	0.907	0.77	0.838	0.781	0.858	2.548	2.916	67.582	145.824

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 8 experiments	median	0.808	0.798	0.645	0.663	0.567	0.593
Overall, 8 experiments	best	0.998	0.996	0.995	0.992	0.963	0.959
Methyl HT-SELEX, 2 experiments	median	0.841	0.837	0.759	0.767	0.672	0.689
Methyl HT-SELEX, 2 experiments	best	0.983	0.974	0.955	0.939	0.829	0.831
Non-Methyl HT-SELEX, 6 experiments	median	0.808	0.798	0.645	0.663	0.567	0.593
Non-Methyl HT-SELEX, 6 experiments	best	0.998	0.996	0.995	0.992	0.963	0.959

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.771	0.618	0.732	0.517

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.H12INVITRO.0.PSM.A.pcm
PWM	SPDEF.H12INVITRO.0.PSM.A.pwm
PFM	SPDEF.H12INVITRO.0.PSM.A.pfm
Alignment	SPDEF.H12INVITRO.0.PSM.A.words.tsv
Threshold to P-value map	SPDEF.H12INVITRO.0.PSM.A.thr
Motif in other formats
JASPAR format	SPDEF.H12INVITRO.0.PSM.A_jaspar_format.txt
MEME format	SPDEF.H12INVITRO.0.PSM.A_meme_format.meme
Transfac format	SPDEF.H12INVITRO.0.PSM.A_transfac_format.txt
Homer format	SPDEF.H12INVITRO.0.PSM.A_homer_format_0.001.txt SPDEF.H12INVITRO.0.PSM.A_homer_format_0.0005.txt SPDEF.H12INVITRO.0.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2911.5	1975.5	2826.5	2227.5
02	5739.75	474.75	634.75	3091.75
03	3469.0	3696.0	1558.0	1218.0
04	210.0	9202.0	514.0	15.0
05	201.0	9728.0	8.0	4.0
06	0.0	0.0	9941.0	0.0
07	0.0	0.0	9939.0	2.0
08	9910.0	2.0	6.0	23.0
09	1157.0	107.0	12.0	8665.0
10	2397.0	1458.0	5641.0	445.0
11	711.5	3263.5	270.5	5695.5
12	2947.0	1677.0	3096.0	2221.0

PFM

	A	C	G	T
01	0.293	0.199	0.284	0.224
02	0.577	0.048	0.064	0.311
03	0.349	0.372	0.157	0.123
04	0.021	0.926	0.052	0.002
05	0.02	0.979	0.001	0.0
06	0.0	0.0	1.0	0.0
07	0.0	0.0	1.0	0.0
08	0.997	0.0	0.001	0.002
09	0.116	0.011	0.001	0.872
10	0.241	0.147	0.567	0.045
11	0.072	0.328	0.027	0.573
12	0.296	0.169	0.311	0.223

PWM

	A	C	G	T
01	0.158	-0.229	0.129	-0.109
02	0.837	-1.651	-1.362	0.218
03	0.333	0.397	-0.466	-0.712
04	-2.461	1.308	-1.572	-4.968
05	-2.504	1.364	-5.487	-5.978
06	-6.986	-6.986	1.386	-6.986
07	-6.986	-6.986	1.385	-6.36
08	1.382	-6.36	-5.703	-4.588
09	-0.763	-3.125	-5.159	1.248
10	-0.036	-0.533	0.819	-1.716
11	-1.248	0.272	-2.21	0.829
12	0.17	-0.393	0.22	-0.112

Standard thresholds

P-value	Threshold
0.001	3.209015
0.0005	4.70274
0.0001	7.41283