PDX1.H12RSNP.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12RSNP.1.PSM.A
Gene (human)	PDX1 (GeneCards)
Gene synonyms (human)	IPF1, STF1
Gene (mouse)	Pdx1
Gene synonyms (mouse)	Ipf1
LOGO
LOGO (reverse complement)
Motif subtype	1
Quality	A

Motif length	12
Consensus	nnvYTAATKAbn
GC content	31.56%
Information content (bits; total / per base)	10.993 / 0.916
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	8954

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	6 (39)	0.603	0.63	0.432	0.459	0.571	0.593	1.347	1.419	35.658	54.585
Mouse	4 (26)	0.643	0.909	0.458	0.848	0.527	0.88	1.246	3.067	30.461	152.155

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.964	0.945	0.921	0.898	0.828	0.822
Overall, 4 experiments	best	0.972	0.953	0.964	0.941	0.952	0.924
Methyl HT-SELEX, 1 experiments	median	0.972	0.953	0.964	0.941	0.952	0.924
Methyl HT-SELEX, 1 experiments	best	0.972	0.953	0.964	0.941	0.952	0.924
Non-Methyl HT-SELEX, 3 experiments	median	0.96	0.943	0.885	0.865	0.718	0.737
Non-Methyl HT-SELEX, 3 experiments	best	0.968	0.946	0.957	0.93	0.939	0.907

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.87	0.635	0.867	0.642

TF superclass	Helix-turn-helix domains {3} (TFClass)
TF class	Homeo domain factors {3.1} (TFClass)
TF family	HOX-related {3.1.1} (TFClass)
TF subfamily	PDX {3.1.1.15} (TFClass)
TFClass ID	TFClass: 3.1.1.15.1
HGNC	HGNC:6107
MGI	MGI:102851
EntrezGene (human)	GeneID:3651 (SSTAR profile)
EntrezGene (mouse)	GeneID:18609 (SSTAR profile)
UniProt ID (human)	PDX1_HUMAN
UniProt ID (mouse)	PDX1_MOUSE
UniProt AC (human)	P52945 (TFClass)
UniProt AC (mouse)	P52946 (TFClass)
GRECO-DB-TF	yes

ChIP-Seq	6 human, 4 mouse
HT-SELEX	3
Methyl-HT-SELEX	1

PCM	PDX1.H12RSNP.1.PSM.A.pcm
PWM	PDX1.H12RSNP.1.PSM.A.pwm
PFM	PDX1.H12RSNP.1.PSM.A.pfm
Alignment	PDX1.H12RSNP.1.PSM.A.words.tsv
Threshold to P-value map	PDX1.H12RSNP.1.PSM.A.thr
Motif in other formats
JASPAR format	PDX1.H12RSNP.1.PSM.A_jaspar_format.txt
MEME format	PDX1.H12RSNP.1.PSM.A_meme_format.meme
Transfac format	PDX1.H12RSNP.1.PSM.A_transfac_format.txt
Homer format	PDX1.H12RSNP.1.PSM.A_homer_format_0.001.txt PDX1.H12RSNP.1.PSM.A_homer_format_0.0005.txt PDX1.H12RSNP.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	2469.0	1879.0	1998.0	2608.0
02	1683.5	3113.5	1718.5	2438.5
03	2695.0	2131.0	3415.0	713.0
04	255.0	4265.0	394.0	4040.0
05	0.0	0.0	0.0	8954.0
06	8954.0	0.0	0.0	0.0
07	8954.0	0.0	0.0	0.0
08	0.0	0.0	0.0	8954.0
09	2.0	205.0	2750.0	5997.0
10	6700.0	110.0	1993.0	151.0
11	1039.5	3777.5	2126.5	2010.5
12	2457.75	2267.75	1771.75	2456.75

PFM

	A	C	G	T
01	0.276	0.21	0.223	0.291
02	0.188	0.348	0.192	0.272
03	0.301	0.238	0.381	0.08
04	0.028	0.476	0.044	0.451
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	0.023	0.307	0.67
10	0.748	0.012	0.223	0.017
11	0.116	0.422	0.237	0.225
12	0.274	0.253	0.198	0.274

PWM

	A	C	G	T
01	0.098	-0.175	-0.114	0.153
02	-0.285	0.33	-0.264	0.085
03	0.185	-0.049	0.422	-1.142
04	-2.164	0.644	-1.732	0.59
05	-6.893	-6.893	-6.893	1.386
06	1.386	-6.893	-6.893	-6.893
07	1.386	-6.893	-6.893	-6.893
08	-6.893	-6.893	-6.893	1.386
09	-6.262	-2.381	0.206	0.985
10	1.096	-2.994	-0.116	-2.682
11	-0.766	0.523	-0.051	-0.107
12	0.093	0.013	-0.234	0.093

Standard thresholds

P-value	Threshold
0.001	4.224725
0.0005	5.66401
0.0001	7.89407