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Gene: PXDN |
Gene summary for PXDN |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PXDN | Gene ID | 7837 |
| Gene name | peroxidasin | |
| Gene Alias | ASGD7 | |
| Cytomap | 2p25.3 | |
| Gene Type | protein-coding | GO ID | GO:0001959 | UniProtAcc | Q92626 |
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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 |
| 7837 | PXDN | P44T-E | Human | Esophagus | ESCC | 1.23e-04 | 3.37e-01 | 0.1096 |
| 7837 | PXDN | P47T-E | Human | Esophagus | ESCC | 1.32e-05 | 2.27e-01 | 0.1067 |
| 7837 | PXDN | P48T-E | Human | Esophagus | ESCC | 4.06e-19 | 4.35e-01 | 0.0959 |
| 7837 | PXDN | P49T-E | Human | Esophagus | ESCC | 1.11e-05 | 6.93e-01 | 0.1768 |
| 7837 | PXDN | P52T-E | Human | Esophagus | ESCC | 4.91e-20 | 4.60e-01 | 0.1555 |
| 7837 | PXDN | P56T-E | Human | Esophagus | ESCC | 5.71e-13 | 1.03e+00 | 0.1613 |
| 7837 | PXDN | P57T-E | Human | Esophagus | ESCC | 1.03e-26 | 6.94e-01 | 0.0926 |
| 7837 | PXDN | P61T-E | Human | Esophagus | ESCC | 3.32e-31 | 6.78e-01 | 0.099 |
| 7837 | PXDN | P62T-E | Human | Esophagus | ESCC | 6.09e-10 | 2.28e-01 | 0.1302 |
| 7837 | PXDN | P65T-E | Human | Esophagus | ESCC | 8.30e-18 | 3.92e-01 | 0.0978 |
| 7837 | PXDN | P74T-E | Human | Esophagus | ESCC | 2.51e-15 | 4.95e-01 | 0.1479 |
| 7837 | PXDN | P76T-E | Human | Esophagus | ESCC | 4.10e-50 | 1.07e+00 | 0.1207 |
| 7837 | PXDN | P79T-E | Human | Esophagus | ESCC | 3.48e-60 | 1.21e+00 | 0.1154 |
| 7837 | PXDN | P83T-E | Human | Esophagus | ESCC | 4.02e-08 | 4.47e-01 | 0.1738 |
| 7837 | PXDN | P84T-E | Human | Esophagus | ESCC | 1.02e-06 | 4.60e-01 | 0.0933 |
| 7837 | PXDN | P91T-E | Human | Esophagus | ESCC | 6.01e-18 | 1.50e+00 | 0.1828 |
| 7837 | PXDN | P126T-E | Human | Esophagus | ESCC | 1.81e-04 | 8.09e-01 | 0.1125 |
| 7837 | PXDN | P130T-E | Human | Esophagus | ESCC | 1.25e-88 | 1.76e+00 | 0.1676 |
| 7837 | PXDN | C30 | Human | Oral cavity | OSCC | 8.08e-30 | 1.18e+00 | 0.3055 |
| 7837 | PXDN | C09 | Human | Oral cavity | OSCC | 1.51e-28 | 9.35e-01 | 0.1431 |
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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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:0006979111 | Esophagus | ESCC | response to oxidative stress | 303/8552 | 446/18723 | 7.15e-22 | 1.30e-19 | 303 |
| GO:00607595 | Esophagus | ESCC | regulation of response to cytokine stimulus | 103/8552 | 162/18723 | 3.14e-06 | 3.53e-05 | 103 |
| GO:00019595 | Esophagus | ESCC | regulation of cytokine-mediated signaling pathway | 95/8552 | 150/18723 | 9.48e-06 | 9.04e-05 | 95 |
| GO:00301984 | Esophagus | ESCC | extracellular matrix organization | 171/8552 | 301/18723 | 6.08e-05 | 4.67e-04 | 171 |
| GO:00430624 | Esophagus | ESCC | extracellular structure organization | 171/8552 | 302/18723 | 7.73e-05 | 5.76e-04 | 171 |
| GO:00452294 | Esophagus | ESCC | external encapsulating structure organization | 172/8552 | 304/18723 | 7.80e-05 | 5.80e-04 | 172 |
| GO:000963620 | Esophagus | ESCC | response to toxic substance | 150/8552 | 262/18723 | 1.00e-04 | 7.12e-04 | 150 |
| GO:007259318 | Esophagus | ESCC | reactive oxygen species metabolic process | 137/8552 | 239/18723 | 1.82e-04 | 1.16e-03 | 137 |
| GO:1990748110 | Esophagus | ESCC | cellular detoxification | 70/8552 | 116/18723 | 1.02e-03 | 5.17e-03 | 70 |
| GO:00301993 | Esophagus | ESCC | collagen fibril organization | 40/8552 | 61/18723 | 1.35e-03 | 6.44e-03 | 40 |
| GO:0097237110 | Esophagus | ESCC | cellular response to toxic substance | 72/8552 | 124/18723 | 3.65e-03 | 1.49e-02 | 72 |
| GO:0098869110 | Esophagus | ESCC | cellular oxidant detoxification | 60/8552 | 101/18723 | 3.76e-03 | 1.53e-02 | 60 |
| GO:00717115 | Esophagus | ESCC | basement membrane organization | 22/8552 | 31/18723 | 3.90e-03 | 1.58e-02 | 22 |
| GO:00850292 | Esophagus | ESCC | extracellular matrix assembly | 29/8552 | 45/18723 | 8.63e-03 | 3.04e-02 | 29 |
| GO:000697920 | Oral cavity | OSCC | response to oxidative stress | 273/7305 | 446/18723 | 8.35e-22 | 1.65e-19 | 273 |
| GO:00019594 | Oral cavity | OSCC | regulation of cytokine-mediated signaling pathway | 87/7305 | 150/18723 | 1.82e-06 | 2.35e-05 | 87 |
| GO:00607594 | Oral cavity | OSCC | regulation of response to cytokine stimulus | 92/7305 | 162/18723 | 3.25e-06 | 3.90e-05 | 92 |
| GO:000963618 | Oral cavity | OSCC | response to toxic substance | 137/7305 | 262/18723 | 7.94e-06 | 8.52e-05 | 137 |
| GO:007259316 | Oral cavity | OSCC | reactive oxygen species metabolic process | 122/7305 | 239/18723 | 9.73e-05 | 7.34e-04 | 122 |
| GO:00192214 | Oral cavity | OSCC | cytokine-mediated signaling pathway | 222/7305 | 472/18723 | 2.02e-04 | 1.35e-03 | 222 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
| PXDN | SNV | Missense_Mutation | novel | c.1537N>T | p.Val513Phe | p.V513F | Q92626 | protein_coding | deleterious(0.03) | possibly_damaging(0.616) | TCGA-BH-A0BW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | adriamycin | CR |
| PXDN | SNV | Missense_Mutation | rs536136666 | c.3542N>T | p.Ala1181Val | p.A1181V | Q92626 | protein_coding | tolerated(0.65) | benign(0.108) | TCGA-BH-A0H7-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD |
| PXDN | SNV | Missense_Mutation | c.2951N>C | p.Leu984Pro | p.L984P | Q92626 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| PXDN | SNV | Missense_Mutation | novel | c.3496N>A | p.Gly1166Arg | p.G1166R | Q92626 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-JL-A3YX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PXDN | insertion | Frame_Shift_Ins | novel | c.672_673insAT | p.Pro225IlefsTer18 | p.P225Ifs*18 | Q92626 | protein_coding | TCGA-A2-A04Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| PXDN | insertion | Nonsense_Mutation | novel | c.3700_3701insAAGCTGACACAGCTTAGAGA | p.Cys1234Ter | p.C1234* | Q92626 | protein_coding | TCGA-A8-A081-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PXDN | insertion | Nonsense_Mutation | novel | c.2003_2004insAATAATTT | p.Tyr668Ter | p.Y668* | Q92626 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PXDN | insertion | Frame_Shift_Ins | novel | c.3901_3902insTATTTAATTTAGTAAGCGTTGAAATCTGCACTGATAATAG | p.Cys1301LeufsTer15 | p.C1301Lfs*15 | Q92626 | protein_coding | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD | ||
| PXDN | SNV | Missense_Mutation | novel | c.1841C>A | p.Pro614His | p.P614H | Q92626 | protein_coding | tolerated(0.06) | possibly_damaging(0.76) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PXDN | SNV | Missense_Mutation | novel | c.1435C>T | p.His479Tyr | p.H479Y | Q92626 | protein_coding | tolerated(0.3) | probably_damaging(0.943) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 |
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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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