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Gene: PRDX4 |
Gene summary for PRDX4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRDX4 | Gene ID | 10549 |
| Gene name | peroxiredoxin 4 | |
| Gene Alias | AOE37-2 | |
| Cytomap | Xp22.11 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q13162 |
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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 |
| 10549 | PRDX4 | GSM4909281 | Human | Breast | IDC | 1.30e-42 | 8.39e-01 | 0.21 |
| 10549 | PRDX4 | GSM4909282 | Human | Breast | IDC | 1.54e-07 | 4.01e-01 | -0.0288 |
| 10549 | PRDX4 | GSM4909285 | Human | Breast | IDC | 1.70e-06 | 3.75e-01 | 0.21 |
| 10549 | PRDX4 | GSM4909286 | Human | Breast | IDC | 8.24e-06 | 3.20e-01 | 0.1081 |
| 10549 | PRDX4 | GSM4909287 | Human | Breast | IDC | 2.58e-02 | 2.35e-01 | 0.2057 |
| 10549 | PRDX4 | GSM4909288 | Human | Breast | IDC | 1.63e-03 | 2.15e-01 | 0.0988 |
| 10549 | PRDX4 | GSM4909296 | Human | Breast | IDC | 8.35e-07 | -4.48e-02 | 0.1524 |
| 10549 | PRDX4 | GSM4909297 | Human | Breast | IDC | 1.91e-10 | -1.44e-01 | 0.1517 |
| 10549 | PRDX4 | GSM4909304 | Human | Breast | IDC | 1.54e-02 | 2.74e-01 | 0.1636 |
| 10549 | PRDX4 | GSM4909308 | Human | Breast | IDC | 1.84e-02 | 1.87e-01 | 0.158 |
| 10549 | PRDX4 | GSM4909311 | Human | Breast | IDC | 1.26e-22 | -2.21e-01 | 0.1534 |
| 10549 | PRDX4 | GSM4909312 | Human | Breast | IDC | 1.79e-09 | 6.02e-02 | 0.1552 |
| 10549 | PRDX4 | GSM4909319 | Human | Breast | IDC | 7.40e-31 | -2.25e-01 | 0.1563 |
| 10549 | PRDX4 | GSM4909320 | Human | Breast | IDC | 1.89e-02 | 5.23e-03 | 0.1575 |
| 10549 | PRDX4 | GSM4909321 | Human | Breast | IDC | 8.16e-13 | 3.06e-02 | 0.1559 |
| 10549 | PRDX4 | brca1 | Human | Breast | Precancer | 2.86e-17 | 5.36e-01 | -0.0338 |
| 10549 | PRDX4 | brca2 | Human | Breast | Precancer | 1.66e-05 | 3.48e-01 | -0.024 |
| 10549 | PRDX4 | M2 | Human | Breast | IDC | 4.31e-02 | 5.33e-02 | 0.21 |
| 10549 | PRDX4 | NCCBC14 | Human | Breast | DCIS | 1.22e-04 | -1.35e-01 | 0.2021 |
| 10549 | PRDX4 | NCCBC5 | Human | Breast | DCIS | 6.84e-09 | 3.99e-02 | 0.2046 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:000697912 | Liver | Cirrhotic | response to oxidative stress | 196/4634 | 446/18723 | 2.80e-19 | 5.86e-17 | 196 |
| GO:00516046 | Liver | Cirrhotic | protein maturation | 121/4634 | 294/18723 | 3.54e-10 | 1.68e-08 | 121 |
| GO:000963612 | Liver | Cirrhotic | response to toxic substance | 104/4634 | 262/18723 | 5.63e-08 | 1.74e-06 | 104 |
| GO:00072494 | Liver | Cirrhotic | I-kappaB kinase/NF-kappaB signaling | 108/4634 | 281/18723 | 2.21e-07 | 5.64e-06 | 108 |
| GO:00725937 | Liver | Cirrhotic | reactive oxygen species metabolic process | 92/4634 | 239/18723 | 1.57e-06 | 3.03e-05 | 92 |
| GO:00987547 | Liver | Cirrhotic | detoxification | 60/4634 | 152/18723 | 4.09e-05 | 4.86e-04 | 60 |
| GO:00972377 | Liver | Cirrhotic | cellular response to toxic substance | 50/4634 | 124/18723 | 9.20e-05 | 9.79e-04 | 50 |
| GO:19907487 | Liver | Cirrhotic | cellular detoxification | 47/4634 | 116/18723 | 1.28e-04 | 1.26e-03 | 47 |
| GO:00182084 | Liver | Cirrhotic | peptidyl-proline modification | 26/4634 | 58/18723 | 6.65e-04 | 5.04e-03 | 26 |
| GO:00614585 | Liver | Cirrhotic | reproductive system development | 132/4634 | 427/18723 | 2.07e-03 | 1.28e-02 | 132 |
| GO:00486085 | Liver | Cirrhotic | reproductive structure development | 131/4634 | 424/18723 | 2.19e-03 | 1.34e-02 | 131 |
| GO:00988697 | Liver | Cirrhotic | cellular oxidant detoxification | 38/4634 | 101/18723 | 2.72e-03 | 1.59e-02 | 38 |
| GO:00454547 | Liver | Cirrhotic | cell redox homeostasis | 16/4634 | 35/18723 | 5.53e-03 | 2.80e-02 | 16 |
| GO:000645712 | Liver | HCC | protein folding | 160/7958 | 212/18723 | 1.07e-22 | 1.88e-20 | 160 |
| GO:000697922 | Liver | HCC | response to oxidative stress | 281/7958 | 446/18723 | 9.75e-19 | 1.24e-16 | 281 |
| GO:005160412 | Liver | HCC | protein maturation | 171/7958 | 294/18723 | 3.80e-08 | 8.30e-07 | 171 |
| GO:000963622 | Liver | HCC | response to toxic substance | 153/7958 | 262/18723 | 1.37e-07 | 2.58e-06 | 153 |
| GO:001820811 | Liver | HCC | peptidyl-proline modification | 42/7958 | 58/18723 | 3.73e-06 | 4.85e-05 | 42 |
| GO:000724912 | Liver | HCC | I-kappaB kinase/NF-kappaB signaling | 156/7958 | 281/18723 | 6.66e-06 | 8.00e-05 | 156 |
| GO:199074812 | Liver | HCC | cellular detoxification | 70/7958 | 116/18723 | 7.87e-05 | 7.02e-04 | 70 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| PRDX4 | SNV | Missense_Mutation | c.785N>C | p.Gly262Ala | p.G262A | Q13162 | protein_coding | tolerated(0.22) | benign(0.018) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRDX4 | deletion | Frame_Shift_Del | novel | c.807delA | p.Lys269AsnfsTer2 | p.K269Nfs*2 | Q13162 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PRDX4 | SNV | Missense_Mutation | novel | c.665N>A | p.Gly222Asp | p.G222D | Q13162 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A7X5-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| PRDX4 | SNV | Missense_Mutation | c.644N>T | p.Thr215Ile | p.T215I | Q13162 | protein_coding | deleterious(0) | possibly_damaging(0.798) | TCGA-A6-4105-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
| PRDX4 | SNV | Missense_Mutation | c.804N>A | p.Asp268Glu | p.D268E | Q13162 | protein_coding | tolerated(1) | benign(0) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRDX4 | SNV | Missense_Mutation | novel | c.319N>T | p.Arg107Cys | p.R107C | Q13162 | protein_coding | deleterious(0) | possibly_damaging(0.882) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PRDX4 | SNV | Missense_Mutation | novel | c.194C>T | p.Ser65Phe | p.S65F | Q13162 | protein_coding | tolerated(0.09) | benign(0.001) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PRDX4 | SNV | Missense_Mutation | novel | c.511C>T | p.Pro171Ser | p.P171S | Q13162 | protein_coding | tolerated(0.32) | benign(0.003) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PRDX4 | SNV | Missense_Mutation | novel | c.8N>T | p.Ala3Val | p.A3V | Q13162 | protein_coding | deleterious_low_confidence(0) | benign(0) | TCGA-AX-A3FT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PRDX4 | SNV | Missense_Mutation | novel | c.319N>T | p.Arg107Cys | p.R107C | Q13162 | protein_coding | deleterious(0) | possibly_damaging(0.882) | TCGA-B5-A0JU-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
| 10549 | PRDX4 | DRUGGABLE GENOME, TRANSCRIPTION FACTOR, ENZYME | docetaxel | DOCETAXEL | 20157331 |
| Page: 1 |
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