|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PDXP |
Gene summary for PDXP |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDXP | Gene ID | 57026 |
| Gene name | pyridoxal phosphatase | |
| Gene Alias | CIN | |
| Cytomap | 22q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | A0A024R1I3 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 57026 | PDXP | HCC1 | Human | Liver | HCC | 3.64e-12 | 2.67e+00 | 0.5336 |
| 57026 | PDXP | HCC2 | Human | Liver | HCC | 3.00e-28 | 4.15e+00 | 0.5341 |
| 57026 | PDXP | S014 | Human | Liver | HCC | 4.58e-05 | 2.08e-01 | 0.2254 |
| 57026 | PDXP | S015 | Human | Liver | HCC | 4.75e-05 | 2.09e-01 | 0.2375 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
| GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
| GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
| GO:001943921 | Liver | HCC | aromatic compound catabolic process | 309/7958 | 467/18723 | 1.56e-25 | 4.94e-23 | 309 |
| GO:002241112 | Liver | HCC | cellular component disassembly | 282/7958 | 443/18723 | 1.02e-19 | 1.38e-17 | 282 |
| GO:004428221 | Liver | HCC | small molecule catabolic process | 225/7958 | 376/18723 | 6.50e-12 | 2.80e-10 | 225 |
| GO:190290322 | Liver | HCC | regulation of supramolecular fiber organization | 224/7958 | 383/18723 | 1.54e-10 | 5.33e-09 | 224 |
| GO:014001411 | Liver | HCC | mitotic nuclear division | 174/7958 | 287/18723 | 3.74e-10 | 1.23e-08 | 174 |
| GO:000701522 | Liver | HCC | actin filament organization | 252/7958 | 442/18723 | 3.83e-10 | 1.25e-08 | 252 |
| GO:190290522 | Liver | HCC | positive regulation of supramolecular fiber organization | 131/7958 | 209/18723 | 2.85e-09 | 7.69e-08 | 131 |
| GO:000734611 | Liver | HCC | regulation of mitotic cell cycle | 255/7958 | 457/18723 | 4.96e-09 | 1.30e-07 | 255 |
| GO:003298411 | Liver | HCC | protein-containing complex disassembly | 138/7958 | 224/18723 | 5.59e-09 | 1.46e-07 | 138 |
| GO:005149522 | Liver | HCC | positive regulation of cytoskeleton organization | 138/7958 | 226/18723 | 1.26e-08 | 3.12e-07 | 138 |
| GO:003253522 | Liver | HCC | regulation of cellular component size | 217/7958 | 383/18723 | 1.28e-08 | 3.14e-07 | 217 |
| GO:003297022 | Liver | HCC | regulation of actin filament-based process | 222/7958 | 397/18723 | 3.81e-08 | 8.30e-07 | 222 |
| GO:003295622 | Liver | HCC | regulation of actin cytoskeleton organization | 202/7958 | 358/18723 | 6.18e-08 | 1.29e-06 | 202 |
| GO:001631121 | Liver | HCC | dephosphorylation | 230/7958 | 417/18723 | 1.00e-07 | 1.96e-06 | 230 |
| GO:000647021 | Liver | HCC | protein dephosphorylation | 162/7958 | 281/18723 | 1.91e-07 | 3.46e-06 | 162 |
| GO:000815422 | Liver | HCC | actin polymerization or depolymerization | 130/7958 | 218/18723 | 2.31e-07 | 4.14e-06 | 130 |
| GO:011005322 | Liver | HCC | regulation of actin filament organization | 158/7958 | 278/18723 | 9.01e-07 | 1.37e-05 | 158 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa012402 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
| hsa012403 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
| Page: 1 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
| PDXP | SNV | Missense_Mutation | novel | c.680N>A | p.Ser227Asn | p.S227N | Q96GD0 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | rs772506359 | c.698N>T | p.Thr233Met | p.T233M | Q96GD0 | protein_coding | deleterious(0.05) | benign(0.127) | TCGA-AP-A1DO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | rs755786722 | c.835N>A | p.Val279Met | p.V279M | Q96GD0 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| PDXP | SNV | Missense_Mutation | novel | c.658N>A | p.Glu220Lys | p.E220K | Q96GD0 | protein_coding | tolerated(0.1) | benign(0.189) | TCGA-FI-A2D6-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | novel | c.538N>A | p.Pro180Thr | p.P180T | Q96GD0 | protein_coding | tolerated(0.77) | benign(0.012) | TCGA-2Y-A9HB-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | novel | c.877G>T | p.Gly293Trp | p.G293W | Q96GD0 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-55-6642-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | novel | c.681C>G | p.Ser227Arg | p.S227R | Q96GD0 | protein_coding | tolerated(0.11) | benign(0.021) | TCGA-NJ-A55A-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PDXP | SNV | Missense_Mutation | c.506N>T | p.Pro169Leu | p.P169L | Q96GD0 | protein_coding | deleterious(0) | benign(0.385) | TCGA-18-3409-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PDXP | SNV | Missense_Mutation | novel | c.870N>C | p.Leu290Phe | p.L290F | Q96GD0 | protein_coding | tolerated(0.23) | benign(0.177) | TCGA-22-5472-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | PD |
| PDXP | SNV | Missense_Mutation | rs747446460 | c.853N>A | p.Glu285Lys | p.E285K | Q96GD0 | protein_coding | tolerated(0.05) | benign(0.124) | TCGA-63-A5MB-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD |
| Page: 1 2 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |