PDX1.H12INVIVO.1.PSM.A motif - HOmo sapiens COmprehensive MOdel COllection

Motif	PDX1.H12INVIVO.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	9
Consensus	dYTAATKRb
GC content	22.74%
Information content (bits; total / per base)	8.793 / 0.977
Data sources	ChIP-Seq + HT-SELEX + Methyl-HT-SELEX
Aligned words	498

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)	0.662	0.708	0.447	0.522	0.646	0.697	1.542	1.846	144.456	178.585
Mouse	4 (26)	0.724	0.9	0.522	0.835	0.646	0.881	1.591	3.303	65.667	161.602

HT-SELEX benchmarking		auROC10	auPRC10	auROC25	auPRC25	auROC50	auPRC50
Overall, 4 experiments	median	0.917	0.864	0.887	0.838	0.801	0.776
Overall, 4 experiments	best	0.929	0.876	0.933	0.881	0.922	0.872
Methyl HT-SELEX, 1 experiments	median	0.929	0.876	0.933	0.881	0.922	0.872
Methyl HT-SELEX, 1 experiments	best	0.929	0.876	0.933	0.881	0.922	0.872
Non-Methyl HT-SELEX, 3 experiments	median	0.912	0.862	0.85	0.808	0.698	0.702
Non-Methyl HT-SELEX, 3 experiments	best	0.923	0.867	0.925	0.869	0.903	0.85

rSNP benchmarking, SNP-SELEX	auROC	auPRC	Pearson r	Kendall tau
batch 2	0.832	0.475	0.861	0.61

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.H12INVIVO.1.PSM.A.pcm
PWM	PDX1.H12INVIVO.1.PSM.A.pwm
PFM	PDX1.H12INVIVO.1.PSM.A.pfm
Alignment	PDX1.H12INVIVO.1.PSM.A.words.tsv
Threshold to P-value map	PDX1.H12INVIVO.1.PSM.A.thr
Motif in other formats
JASPAR format	PDX1.H12INVIVO.1.PSM.A_jaspar_format.txt
MEME format	PDX1.H12INVIVO.1.PSM.A_meme_format.meme
Transfac format	PDX1.H12INVIVO.1.PSM.A_transfac_format.txt
Homer format	PDX1.H12INVIVO.1.PSM.A_homer_format_0.001.txt PDX1.H12INVIVO.1.PSM.A_homer_format_0.0005.txt PDX1.H12INVIVO.1.PSM.A_homer_format_0.0001.txt

PCM

	A	C	G	T
01	259.0	21.0	98.0	120.0
02	13.0	80.0	63.0	342.0
03	43.0	6.0	3.0	446.0
04	423.0	14.0	57.0	4.0
05	484.0	4.0	9.0	1.0
06	13.0	3.0	39.0	443.0
07	4.0	4.0	195.0	295.0
08	327.0	8.0	149.0	14.0
09	41.0	143.0	123.0	191.0

PFM

	A	C	G	T
01	0.52	0.042	0.197	0.241
02	0.026	0.161	0.127	0.687
03	0.086	0.012	0.006	0.896
04	0.849	0.028	0.114	0.008
05	0.972	0.008	0.018	0.002
06	0.026	0.006	0.078	0.89
07	0.008	0.008	0.392	0.592
08	0.657	0.016	0.299	0.028
09	0.082	0.287	0.247	0.384

PWM

	A	C	G	T
01	0.726	-1.721	-0.236	-0.036
02	-2.159	-0.435	-0.669	1.003
03	-1.04	-2.815	-3.321	1.267
04	1.214	-2.092	-0.767	-3.122
05	1.349	-3.122	-2.48	-3.9
06	-2.159	-3.321	-1.134	1.26
07	-3.122	-3.122	0.444	0.856
08	0.958	-2.58	0.178	-2.092
09	-1.086	0.137	-0.012	0.424

Standard thresholds

P-value	Threshold
0.001	5.00077
0.0005	5.823595
0.0001	7.36158