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Gene: PXMP4 |
Gene summary for PXMP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PXMP4 | Gene ID | 11264 |
| Gene name | peroxisomal membrane protein 4 | |
| Gene Alias | PMP24 | |
| Cytomap | 20q11.22 | |
| Gene Type | protein-coding | GO ID | GO:0008150 | UniProtAcc | Q9Y6I8 |
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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 |
| 11264 | PXMP4 | LZE22T | Human | Esophagus | ESCC | 1.07e-02 | 2.32e-01 | 0.068 |
| 11264 | PXMP4 | LZE24T | Human | Esophagus | ESCC | 8.96e-21 | 5.57e-01 | 0.0596 |
| 11264 | PXMP4 | LZE21T | Human | Esophagus | ESCC | 4.93e-02 | 1.86e-01 | 0.0655 |
| 11264 | PXMP4 | P2T-E | Human | Esophagus | ESCC | 2.05e-02 | 1.08e-01 | 0.1177 |
| 11264 | PXMP4 | P4T-E | Human | Esophagus | ESCC | 6.30e-14 | 3.61e-01 | 0.1323 |
| 11264 | PXMP4 | P5T-E | Human | Esophagus | ESCC | 2.04e-08 | 1.74e-01 | 0.1327 |
| 11264 | PXMP4 | P8T-E | Human | Esophagus | ESCC | 1.89e-14 | 2.59e-01 | 0.0889 |
| 11264 | PXMP4 | P9T-E | Human | Esophagus | ESCC | 4.68e-02 | 1.15e-01 | 0.1131 |
| 11264 | PXMP4 | P10T-E | Human | Esophagus | ESCC | 9.69e-20 | 3.45e-01 | 0.116 |
| 11264 | PXMP4 | P11T-E | Human | Esophagus | ESCC | 2.07e-02 | 1.73e-01 | 0.1426 |
| 11264 | PXMP4 | P12T-E | Human | Esophagus | ESCC | 6.05e-10 | 2.98e-01 | 0.1122 |
| 11264 | PXMP4 | P15T-E | Human | Esophagus | ESCC | 1.97e-07 | 1.77e-01 | 0.1149 |
| 11264 | PXMP4 | P16T-E | Human | Esophagus | ESCC | 2.73e-09 | 2.34e-01 | 0.1153 |
| 11264 | PXMP4 | P17T-E | Human | Esophagus | ESCC | 3.09e-09 | 3.38e-01 | 0.1278 |
| 11264 | PXMP4 | P20T-E | Human | Esophagus | ESCC | 3.78e-04 | 1.76e-01 | 0.1124 |
| 11264 | PXMP4 | P21T-E | Human | Esophagus | ESCC | 4.92e-23 | 4.52e-01 | 0.1617 |
| 11264 | PXMP4 | P22T-E | Human | Esophagus | ESCC | 9.06e-07 | 1.37e-01 | 0.1236 |
| 11264 | PXMP4 | P23T-E | Human | Esophagus | ESCC | 4.12e-10 | 2.50e-01 | 0.108 |
| 11264 | PXMP4 | P24T-E | Human | Esophagus | ESCC | 8.76e-13 | 2.68e-01 | 0.1287 |
| 11264 | PXMP4 | P26T-E | Human | Esophagus | ESCC | 1.02e-15 | 3.66e-01 | 0.1276 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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. |
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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 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa041467 | Esophagus | ESCC | Peroxisome | 55/4205 | 82/8465 | 1.04e-03 | 3.27e-03 | 1.68e-03 | 55 |
| hsa0414612 | Esophagus | ESCC | Peroxisome | 55/4205 | 82/8465 | 1.04e-03 | 3.27e-03 | 1.68e-03 | 55 |
| hsa041464 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa041465 | Liver | HCC | Peroxisome | 58/4020 | 82/8465 | 1.57e-05 | 1.05e-04 | 5.85e-05 | 58 |
| hsa041466 | Oral cavity | OSCC | Peroxisome | 47/3704 | 82/8465 | 9.01e-03 | 2.01e-02 | 1.03e-02 | 47 |
| hsa0414611 | Oral cavity | OSCC | Peroxisome | 47/3704 | 82/8465 | 9.01e-03 | 2.01e-02 | 1.03e-02 | 47 |
| hsa0414621 | Oral cavity | LP | Peroxisome | 33/2418 | 82/8465 | 1.48e-02 | 4.69e-02 | 3.03e-02 | 33 |
| hsa0414631 | Oral cavity | LP | Peroxisome | 33/2418 | 82/8465 | 1.48e-02 | 4.69e-02 | 3.03e-02 | 33 |
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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 |
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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 |
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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 |
| PXMP4 | SNV | Missense_Mutation | c.125A>G | p.Lys42Arg | p.K42R | Q9Y6I8 | protein_coding | tolerated(0.06) | possibly_damaging(0.67) | TCGA-A8-A08F-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| PXMP4 | SNV | Missense_Mutation | novel | c.542N>T | p.Ser181Leu | p.S181L | Q9Y6I8 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A0B0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| PXMP4 | SNV | Missense_Mutation | c.527C>T | p.Ser176Phe | p.S176F | Q9Y6I8 | protein_coding | deleterious(0.02) | benign(0.044) | TCGA-E2-A10C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| PXMP4 | SNV | Missense_Mutation | rs182672515 | c.524N>A | p.Arg175Gln | p.R175Q | Q9Y6I8 | protein_coding | tolerated(0.29) | benign(0.014) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PXMP4 | SNV | Missense_Mutation | novel | c.357C>A | p.Asn119Lys | p.N119K | Q9Y6I8 | protein_coding | tolerated(0.21) | benign(0.216) | TCGA-AJ-A3NF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | chemo | CR |
| PXMP4 | SNV | Missense_Mutation | novel | c.281A>G | p.Tyr94Cys | p.Y94C | Q9Y6I8 | protein_coding | tolerated(0.16) | benign(0) | TCGA-AJ-A8CW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PXMP4 | SNV | Missense_Mutation | c.419G>A | p.Arg140His | p.R140H | Q9Y6I8 | protein_coding | deleterious(0) | benign(0.16) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PXMP4 | SNV | Missense_Mutation | c.335N>A | p.Gly112Asp | p.G112D | Q9Y6I8 | protein_coding | deleterious(0) | probably_damaging(0.951) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PXMP4 | SNV | Missense_Mutation | novel | c.616A>G | p.Asn206Asp | p.N206D | Q9Y6I8 | protein_coding | deleterious(0.02) | probably_damaging(0.965) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PXMP4 | SNV | Missense_Mutation | c.265N>T | p.Arg89Cys | p.R89C | Q9Y6I8 | protein_coding | tolerated(0.65) | benign(0) | TCGA-D1-A177-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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 |
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