Gene: PDXP

LinkedOmicsKB © 2022-2023 Zhang Lab

Basic information

Full name
pyridoxal phosphatase
Ensembl
ENSG00000241360.2
Summary
Pyridoxal 5-prime-phosphate (PLP) is the active form of vitamin B6 that acts as a coenzyme in maintaining biochemical homeostasis. The preferred degradation route from PLP to 4-pyridoxic acid involves the dephosphorylation of PLP by PDXP (Jang et al., 2003 [PubMed 14522954]).[supplied by OMIM, Mar 2008]
Annotation
Phosphatase

Protein product

Phosphosites on the primary protein product

Tumor and normal comparison

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Signed p-values
Data type
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
RNA9.6e-8--7.7e-7--7.8e-32.3e-96.6e-22--0.17-
protein-8.6e-49-3.5e-15-3.5e-24--1.7e-4-6.6e-18-1.2e-28-1.1e-6-1.2e-13-5.0e-4

* P-values are from Wilcoxon rank sum test and can be clicked to show the box plots. Positive values mean higher abundance in tumor. BRCA and GBM do not have normal samples.

mRNA expression at gene level
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC23456789101112log2(RSEM+1)tumornormal
Protein expression
BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC21.52222.52323.52424.52525.52626.52727.528log2(MS1 intensity)tumornormal

* Mild outlier: filled circle; Extreme outlier: empty circle.

Phenotype and mutation association

Manhattan plot summarizing associations of phenotypes and mutations across all cohorts and omics data types

BRCACCRCCCOADGBMHNSCCLSCCLUADOVPDACUCEC02468101214160-2-4-6-8-10-12-14-16Pan-cancer0246810121416182022242628300-2-4-6-8-10-12-14-16-18-20-22-24-26-28-30proteinRNASCNVclinicalpathwaycell typegenomicmutation-log10 of P-value

* Data points of significant associations above and below the dotted lines can be hovered to show the phenotype.

Associations of the protein abundance of PDXP with phenotypes and mutations

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Signed p-values
Phenotype
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
DISEASE-PSP_Alzheimer's_disease8.2e-11---2.2e-16-----0.33
KINASE-PSP_CDK52.9e-7---7.8e-60.380.012--0.180.024
HALLMARK_HEDGEHOG_SIGNALING1.9e-50.27-0.850.535.2e-31.4e-40.580.670.180.0140.54
HALLMARK_PANCREAS_BETA_CELLS1.4e-40.120.89-0.348.7e-90.44-0.340.0530.520.0290.34
xcell: Cancer associated fibroblast4.1e-4-0.1-0.82.9e-3-0.21.0e-40.0780.760.391.2e-30.19
xcell: Hematopoietic stem cell5.6e-4-0.120.180.350.040.0060.250.82-0.717.2e-30.086
xcell: stroma score1.5e-3-0.0240.713.4e-3-0.0919.2e-40.140.380.524.9e-30.12
PROGENy: Estrogen2.3e-3-0.220.0970.06-0.780.020.632.4e-30.470.25-0.93
HALLMARK_MYOGENESIS3.2e-3-0.060.492.5e-3-0.146.1e-30.520.670.230.352.4e-3
PROGENy: Trail3.4e-3-0.93-0.310.060.171.1e-50.810.920.520.40.37
Showing 1 to 10 of 256 rows

* P-values could be from test for Spearman correlation, Wilcoxon rank sum test, Jonckheere-Terpstra trend test or Cox regression depending on the data type. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Cis-association

Associations between omics data of PDXP

BRCA0.440.500.34proteinmRNASCNVmethylationCCRCC0.56-0.030.230.020.06-0.08proteinmRNASCNVmethylationCOAD0.290.180.09proteinmRNASCNVmethylationGBM0.660.080.240.110.25-0.06proteinmRNASCNVmethylationHNSCC0.50-0.190.26-0.140.140.01proteinmRNASCNVmethylationLSCC0.600.010.200.030.130.09proteinmRNASCNVmethylationLUAD0.12-0.130.24-0.110.16-0.05proteinmRNASCNVmethylationOV0.320.340.14proteinmRNASCNVmethylationPDAC0.08-0.26-0.12-0.120.080.10proteinmRNASCNVmethylationUCEC0.29-0.050.110.040.14-0.14proteinmRNASCNVmethylation

* The numbers are Spearman correlation coefficients and can be clicked to show the scatter plots. The color and size of the circles correlate with the coefficients.

Trans-association

Associations of the protein abundance of PDXP and the protein abundance of other genes

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Signed p-values
Gene
Meta P
BRCA
CCRCC
COAD
GBM
HNSCC
LSCC
LUAD
OV
PDAC
UCEC
No matching records found

* P-values are from test for Spearman correlation. P-values for individual cohorts can be clicked to show the data plots. The matrix icons in each row can be clicked to show a heatmap summary of associations across all cohorts and omics. The rows in the table can be expanded to show results from other omics.

Gene set enrichment analysis

Submit genes and the common logarithm of the p-values of their association with to WebGestalt.