KLF12.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	KLF12.H12RSNP.1.PSM.A
Gene (human)	KLF12 (GeneCards)
Gene synonyms (human)	AP2REP
Gene (mouse)	Klf12
Gene synonyms (mouse)	Ap2rep
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	13
Consensus	dddGGGCGTGGYv
GC content	70.36%
Information content (bits; total / per base)	14.558 / 1.12
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	9706

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	1 (5)	0.811	0.83	0.69	0.713	0.793	0.811	2.755	2.814	96.387	122.444

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.804	0.804	0.734	0.735	0.646	0.657
Overall, 4 experiments	best	0.997	0.995	0.995	0.992	0.977	0.972
Methyl HT-SELEX, 1 experiments	median	0.997	0.995	0.995	0.992	0.977	0.972
Methyl HT-SELEX, 1 experiments	best	0.997	0.995	0.995	0.992	0.977	0.972
Non-Methyl HT-SELEX, 3 experiments	median	0.623	0.632	0.554	0.567	0.526	0.538
Non-Methyl HT-SELEX, 3 experiments	best	0.984	0.976	0.914	0.904	0.766	0.777

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 1	0.872	0.426	0.858	0.529
batch 2	0.802	0.428	0.731	0.524

TF superclass	Zinc-coordinating DNA-binding domains {2} (TFClass)
TF class	C2H2 zinc finger factors {2.3} (TFClass)
TF family	Three-zinc finger Kruppel-related {2.3.1} (TFClass)
TF subfamily	Kr-like {2.3.1.2} (TFClass)
TFClass ID	TFClass: 2.3.1.2.12
HGNC	HGNC:6346
MGI	MGI:1333796
EntrezGene (human)	GeneID:11278 (SSTAR profile)
EntrezGene (mouse)	GeneID:16597 (SSTAR profile)
UniProt ID (human)	KLF12_HUMAN
UniProt ID (mouse)	KLF12_MOUSE
UniProt AC (human)	Q9Y4X4 (TFClass)
UniProt AC (mouse)	O35738 (TFClass)
GRECO-DB-TF	yes

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

PCM	KLF12.H12RSNP.1.PSM.A.pcm
PWM	KLF12.H12RSNP.1.PSM.A.pwm
PFM	KLF12.H12RSNP.1.PSM.A.pfm
Alignment	KLF12.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	KLF12.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	KLF12.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	KLF12.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	KLF12.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	KLF12.H12RSNP.1.PSM.A_homer_format_0.001.txt KLF12.H12RSNP.1.PSM.A_homer_format_0.0005.txt KLF12.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2089.0	1473.0	3774.0	2370.0
02	2836.75	936.75	3542.75	2389.75
03	3395.0	205.0	2101.0	4005.0
04	466.0	65.0	8980.0	195.0
05	78.0	189.0	9368.0	71.0
06	52.0	6.0	9591.0	57.0
07	51.0	9136.0	67.0	452.0
08	24.0	3.0	9678.0	1.0
09	110.0	54.0	222.0	9320.0
10	199.0	70.0	9182.0	255.0
11	350.0	197.0	8802.0	357.0
12	382.75	4071.75	1059.75	4191.75
13	1880.5	4135.5	1864.5	1825.5

PFM

	A	C	G	T
01	0.215	0.152	0.389	0.244
02	0.292	0.097	0.365	0.246
03	0.35	0.021	0.216	0.413
04	0.048	0.007	0.925	0.02
05	0.008	0.019	0.965	0.007
06	0.005	0.001	0.988	0.006
07	0.005	0.941	0.007	0.047
08	0.002	0.0	0.997	0.0
09	0.011	0.006	0.023	0.96
10	0.021	0.007	0.946	0.026
11	0.036	0.02	0.907	0.037
12	0.039	0.42	0.109	0.432
13	0.194	0.426	0.192	0.188

PWM

	A	C	G	T
01	-0.15	-0.499	0.441	-0.024
02	0.156	-0.95	0.378	-0.015
03	0.336	-2.461	-0.144	0.501
04	-1.646	-3.586	1.308	-2.51
05	-3.409	-2.541	1.35	-3.501
06	-3.801	-5.679	1.374	-3.713
07	-3.819	1.325	-3.557	-1.676
08	-4.526	-6.128	1.383	-6.603
09	-3.074	-3.765	-2.382	1.345
10	-2.49	-3.514	1.33	-2.245
11	-1.931	-2.5	1.288	-1.911
12	-1.842	0.517	-0.827	0.546
13	-0.255	0.533	-0.263	-0.284

Standard thresholds

P-value	Threshold
0.001	2.64886
0.0005	3.85156
0.0001	6.630455