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Gene: PEX13 |
Gene summary for PEX13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PEX13 | Gene ID | 5194 |
| Gene name | peroxisomal biogenesis factor 13 | |
| Gene Alias | NALD | |
| Cytomap | 2p15 | |
| Gene Type | protein-coding | GO ID | GO:0001561 | UniProtAcc | Q92968 |
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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 |
| 5194 | PEX13 | C46 | Human | Oral cavity | OSCC | 6.19e-16 | 3.53e-01 | 0.1673 |
| 5194 | PEX13 | C51 | Human | Oral cavity | OSCC | 7.92e-06 | 4.86e-01 | 0.2674 |
| 5194 | PEX13 | C57 | Human | Oral cavity | OSCC | 1.41e-12 | 3.85e-01 | 0.1679 |
| 5194 | PEX13 | C06 | Human | Oral cavity | OSCC | 2.00e-04 | 7.54e-01 | 0.2699 |
| 5194 | PEX13 | C07 | Human | Oral cavity | OSCC | 2.47e-05 | 1.21e+00 | 0.2491 |
| 5194 | PEX13 | C08 | Human | Oral cavity | OSCC | 7.81e-40 | 7.79e-01 | 0.1919 |
| 5194 | PEX13 | C09 | Human | Oral cavity | OSCC | 3.81e-02 | 1.33e-01 | 0.1431 |
| 5194 | PEX13 | LN22 | Human | Oral cavity | OSCC | 8.15e-09 | 8.35e-01 | 0.1733 |
| 5194 | PEX13 | LN46 | Human | Oral cavity | OSCC | 1.71e-05 | 3.30e-01 | 0.1666 |
| 5194 | PEX13 | LP15 | Human | Oral cavity | LP | 3.16e-06 | 1.39e+00 | 0.2174 |
| 5194 | PEX13 | LP17 | Human | Oral cavity | LP | 7.70e-04 | 5.76e-01 | 0.2349 |
| 5194 | PEX13 | SYSMH1 | Human | Oral cavity | OSCC | 1.95e-11 | 3.36e-01 | 0.1127 |
| 5194 | PEX13 | SYSMH2 | Human | Oral cavity | OSCC | 5.32e-14 | 4.29e-01 | 0.2326 |
| 5194 | PEX13 | SYSMH3 | Human | Oral cavity | OSCC | 9.36e-14 | 4.90e-01 | 0.2442 |
| 5194 | PEX13 | SYSMH5 | Human | Oral cavity | OSCC | 9.17e-03 | 7.37e-02 | 0.0647 |
| 5194 | PEX13 | SYSMH6 | Human | Oral cavity | OSCC | 6.57e-03 | 1.98e-01 | 0.1275 |
| 5194 | PEX13 | P5_S10_cSCC | Human | Skin | cSCC | 3.25e-08 | 2.22e-01 | -0.299 |
| 5194 | PEX13 | P1_cSCC | Human | Skin | cSCC | 7.02e-11 | 4.34e-01 | 0.0292 |
| 5194 | PEX13 | P2_cSCC | Human | Skin | cSCC | 7.27e-05 | 2.20e-01 | -0.024 |
| 5194 | PEX13 | P4_cSCC | Human | Skin | cSCC | 1.94e-04 | 2.88e-01 | -0.00290000000000005 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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 |
| GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:001703818 | Esophagus | ESCC | protein import | 149/8552 | 206/18723 | 5.90e-15 | 3.31e-13 | 149 |
| GO:00718069 | Esophagus | ESCC | protein transmembrane transport | 47/8552 | 59/18723 | 9.02e-08 | 1.51e-06 | 47 |
| GO:00650026 | Esophagus | ESCC | intracellular protein transmembrane transport | 40/8552 | 51/18723 | 1.76e-06 | 2.08e-05 | 40 |
| GO:00193958 | Esophagus | ESCC | fatty acid oxidation | 69/8552 | 103/18723 | 9.95e-06 | 9.44e-05 | 69 |
| GO:00447433 | Esophagus | ESCC | protein transmembrane import into intracellular organelle | 29/8552 | 36/18723 | 1.91e-05 | 1.67e-04 | 29 |
| GO:00344407 | Esophagus | ESCC | lipid oxidation | 71/8552 | 108/18723 | 2.00e-05 | 1.74e-04 | 71 |
| GO:00090628 | Esophagus | ESCC | fatty acid catabolic process | 66/8552 | 100/18723 | 3.21e-05 | 2.66e-04 | 66 |
| GO:00066318 | Esophagus | ESCC | fatty acid metabolic process | 217/8552 | 390/18723 | 4.21e-05 | 3.39e-04 | 217 |
| GO:00723297 | Esophagus | ESCC | monocarboxylic acid catabolic process | 74/8552 | 122/18723 | 6.03e-04 | 3.27e-03 | 74 |
| GO:00442427 | Esophagus | ESCC | cellular lipid catabolic process | 121/8552 | 214/18723 | 8.63e-04 | 4.43e-03 | 121 |
| GO:00442827 | Esophagus | ESCC | small molecule catabolic process | 201/8552 | 376/18723 | 1.35e-03 | 6.41e-03 | 201 |
| GO:00302586 | Esophagus | ESCC | lipid modification | 116/8552 | 212/18723 | 4.90e-03 | 1.89e-02 | 116 |
| GO:00066252 | Esophagus | ESCC | protein targeting to peroxisome | 14/8552 | 18/18723 | 5.77e-03 | 2.14e-02 | 14 |
| GO:00726622 | Esophagus | ESCC | protein localization to peroxisome | 14/8552 | 18/18723 | 5.77e-03 | 2.14e-02 | 14 |
| GO:00726632 | Esophagus | ESCC | establishment of protein localization to peroxisome | 14/8552 | 18/18723 | 5.77e-03 | 2.14e-02 | 14 |
| GO:00215436 | Esophagus | ESCC | pallium development | 94/8552 | 169/18723 | 5.79e-03 | 2.14e-02 | 94 |
| GO:00160427 | Esophagus | ESCC | lipid catabolic process | 168/8552 | 320/18723 | 7.97e-03 | 2.84e-02 | 168 |
| GO:00435742 | Esophagus | ESCC | peroxisomal transport | 16/8552 | 22/18723 | 9.46e-03 | 3.28e-02 | 16 |
| Page: 1 2 3 4 5 |
| 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 |
| hsa04146 | Liver | NAFLD | Peroxisome | 19/1043 | 82/8465 | 4.37e-03 | 4.10e-02 | 3.30e-02 | 19 |
| hsa041461 | Liver | NAFLD | Peroxisome | 19/1043 | 82/8465 | 4.37e-03 | 4.10e-02 | 3.30e-02 | 19 |
| 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 |
| PEX13 | SNV | Missense_Mutation | novel | c.374N>C | p.Ser125Thr | p.S125T | Q92968 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PEX13 | SNV | Missense_Mutation | c.1114N>A | p.Glu372Lys | p.E372K | Q92968 | protein_coding | tolerated(0.09) | benign(0.021) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PEX13 | SNV | Missense_Mutation | c.31N>T | p.Pro11Ser | p.P11S | Q92968 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-AN-A0FL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PEX13 | SNV | Missense_Mutation | c.341N>G | p.Pro114Arg | p.P114R | Q92968 | protein_coding | tolerated(0.15) | probably_damaging(0.959) | TCGA-EW-A1IY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| PEX13 | insertion | Frame_Shift_Ins | novel | c.304_305insCTGTTATCCTGACATTTTGGGA | p.Gly102AlafsTer18 | p.G102Afs*18 | Q92968 | protein_coding | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PEX13 | SNV | Missense_Mutation | c.635N>T | p.Ala212Val | p.A212V | Q92968 | protein_coding | tolerated(0.08) | benign(0.068) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PEX13 | SNV | Missense_Mutation | novel | c.206N>C | p.Asn69Thr | p.N69T | Q92968 | protein_coding | tolerated(0.24) | benign(0.079) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PEX13 | SNV | Missense_Mutation | c.41C>T | p.Thr14Ile | p.T14I | Q92968 | protein_coding | tolerated(0.12) | benign(0.063) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR | |
| PEX13 | SNV | Missense_Mutation | c.983N>T | p.Ala328Val | p.A328V | Q92968 | protein_coding | deleterious(0.02) | benign(0.209) | TCGA-AG-3591-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unspecific | Complete Response | ||
| PEX13 | SNV | Missense_Mutation | novel | c.110N>A | p.Pro37His | p.P37H | Q92968 | protein_coding | deleterious(0.04) | possibly_damaging(0.628) | TCGA-AG-3726-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
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