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Gene: PRDX2 |
Gene summary for PRDX2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRDX2 | Gene ID | 7001 |
| Gene name | peroxiredoxin 2 | |
| Gene Alias | HEL-S-2a | |
| Cytomap | 19p13.13 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P32119 |
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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 |
| 7001 | PRDX2 | GSM4909281 | Human | Breast | IDC | 1.18e-02 | 3.08e-01 | 0.21 |
| 7001 | PRDX2 | GSM4909282 | Human | Breast | IDC | 6.87e-39 | 6.09e-01 | -0.0288 |
| 7001 | PRDX2 | GSM4909285 | Human | Breast | IDC | 4.48e-60 | 8.36e-01 | 0.21 |
| 7001 | PRDX2 | GSM4909286 | Human | Breast | IDC | 6.82e-03 | 1.06e-01 | 0.1081 |
| 7001 | PRDX2 | GSM4909287 | Human | Breast | IDC | 4.67e-12 | 3.41e-01 | 0.2057 |
| 7001 | PRDX2 | GSM4909289 | Human | Breast | IDC | 7.11e-06 | 4.58e-01 | 0.1064 |
| 7001 | PRDX2 | GSM4909290 | Human | Breast | IDC | 2.92e-18 | 5.08e-01 | 0.2096 |
| 7001 | PRDX2 | GSM4909291 | Human | Breast | IDC | 1.69e-03 | 2.53e-01 | 0.1753 |
| 7001 | PRDX2 | GSM4909293 | Human | Breast | IDC | 5.60e-14 | 4.91e-01 | 0.1581 |
| 7001 | PRDX2 | GSM4909294 | Human | Breast | IDC | 7.78e-26 | 4.87e-01 | 0.2022 |
| 7001 | PRDX2 | GSM4909296 | Human | Breast | IDC | 1.93e-27 | 3.68e-01 | 0.1524 |
| 7001 | PRDX2 | GSM4909297 | Human | Breast | IDC | 2.46e-22 | 1.06e-01 | 0.1517 |
| 7001 | PRDX2 | GSM4909301 | Human | Breast | IDC | 2.42e-04 | 2.52e-01 | 0.1577 |
| 7001 | PRDX2 | GSM4909302 | Human | Breast | IDC | 2.82e-07 | 2.14e-01 | 0.1545 |
| 7001 | PRDX2 | GSM4909304 | Human | Breast | IDC | 6.66e-42 | 7.09e-01 | 0.1636 |
| 7001 | PRDX2 | GSM4909305 | Human | Breast | IDC | 1.98e-02 | 1.96e-01 | 0.0436 |
| 7001 | PRDX2 | GSM4909306 | Human | Breast | IDC | 1.79e-20 | 5.49e-01 | 0.1564 |
| 7001 | PRDX2 | GSM4909307 | Human | Breast | IDC | 1.45e-15 | 4.35e-01 | 0.1569 |
| 7001 | PRDX2 | GSM4909308 | Human | Breast | IDC | 2.01e-34 | 6.23e-01 | 0.158 |
| 7001 | PRDX2 | GSM4909309 | Human | Breast | IDC | 4.81e-02 | 9.66e-02 | 0.0483 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:199074816 | Prostate | BPH | cellular detoxification | 34/3107 | 116/18723 | 4.40e-04 | 3.16e-03 | 34 |
| GO:00510906 | Prostate | BPH | regulation of DNA-binding transcription factor activity | 100/3107 | 440/18723 | 4.71e-04 | 3.37e-03 | 100 |
| GO:000715910 | Prostate | BPH | leukocyte cell-cell adhesion | 86/3107 | 371/18723 | 5.95e-04 | 4.11e-03 | 86 |
| GO:009875416 | Prostate | BPH | detoxification | 41/3107 | 152/18723 | 8.07e-04 | 5.27e-03 | 41 |
| GO:004545415 | Prostate | BPH | cell redox homeostasis | 14/3107 | 35/18723 | 8.33e-04 | 5.41e-03 | 14 |
| GO:200037710 | Prostate | BPH | regulation of reactive oxygen species metabolic process | 42/3107 | 157/18723 | 8.41e-04 | 5.46e-03 | 42 |
| GO:190303710 | Prostate | BPH | regulation of leukocyte cell-cell adhesion | 78/3107 | 336/18723 | 9.95e-04 | 6.25e-03 | 78 |
| GO:003249615 | Prostate | BPH | response to lipopolysaccharide | 79/3107 | 343/18723 | 1.18e-03 | 7.29e-03 | 79 |
| GO:005086310 | Prostate | BPH | regulation of T cell activation | 76/3107 | 329/18723 | 1.32e-03 | 7.95e-03 | 76 |
| GO:00380345 | Prostate | BPH | signal transduction in absence of ligand | 21/3107 | 65/18723 | 1.37e-03 | 8.19e-03 | 21 |
| GO:00971925 | Prostate | BPH | extrinsic apoptotic signaling pathway in absence of ligand | 21/3107 | 65/18723 | 1.37e-03 | 8.19e-03 | 21 |
| GO:00485384 | Prostate | BPH | thymus development | 16/3107 | 45/18723 | 1.62e-03 | 9.39e-03 | 16 |
| GO:00075968 | Prostate | BPH | blood coagulation | 53/3107 | 217/18723 | 1.91e-03 | 1.09e-02 | 53 |
| GO:00508178 | Prostate | BPH | coagulation | 54/3107 | 222/18723 | 1.92e-03 | 1.09e-02 | 54 |
| GO:000223715 | Prostate | BPH | response to molecule of bacterial origin | 81/3107 | 363/18723 | 2.63e-03 | 1.41e-02 | 81 |
| GO:00300982 | Prostate | BPH | lymphocyte differentiation | 83/3107 | 374/18723 | 2.76e-03 | 1.46e-02 | 83 |
| GO:00075998 | Prostate | BPH | hemostasis | 53/3107 | 222/18723 | 3.21e-03 | 1.67e-02 | 53 |
| GO:00456193 | Prostate | BPH | regulation of lymphocyte differentiation | 43/3107 | 174/18723 | 3.84e-03 | 1.92e-02 | 43 |
| GO:00302174 | Prostate | BPH | T cell differentiation | 58/3107 | 257/18723 | 7.66e-03 | 3.39e-02 | 58 |
| GO:00224085 | Prostate | BPH | negative regulation of cell-cell adhesion | 46/3107 | 196/18723 | 7.95e-03 | 3.47e-02 | 46 |
| 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 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 |
| 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 |
| PRDX2 | SNV | Missense_Mutation | novel | c.544A>T | p.Thr182Ser | p.T182S | P32119 | protein_coding | deleterious(0.03) | possibly_damaging(0.515) | TCGA-A7-A4SA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| PRDX2 | SNV | Missense_Mutation | novel | c.565N>T | p.Asp189Tyr | p.D189Y | P32119 | protein_coding | deleterious(0.01) | benign(0.102) | TCGA-OL-A66L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PRDX2 | insertion | Frame_Shift_Ins | novel | c.245_246insGGGAGGAGGTTGCAGTAAG | p.His83GlyfsTer30 | p.H83Gfs*30 | P32119 | protein_coding | TCGA-A2-A0EV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PRDX2 | SNV | Missense_Mutation | novel | c.169N>A | p.Ala57Thr | p.A57T | P32119 | protein_coding | deleterious(0.01) | probably_damaging(0.97) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PRDX2 | SNV | Missense_Mutation | novel | c.452C>T | p.Ser151Phe | p.S151F | P32119 | protein_coding | deleterious(0.03) | probably_damaging(0.996) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PRDX2 | SNV | Missense_Mutation | rs534702204 | c.334T>C | p.Ser112Pro | p.S112P | P32119 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PRDX2 | SNV | Missense_Mutation | rs755166073 | c.448N>T | p.Arg150Cys | p.R150C | P32119 | protein_coding | deleterious(0.05) | probably_damaging(0.98) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| PRDX2 | SNV | Missense_Mutation | rs764907738 | c.559N>A | p.Val187Met | p.V187M | P32119 | protein_coding | tolerated(0.06) | benign(0.376) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PRDX2 | SNV | Missense_Mutation | rs369634820 | c.272G>A | p.Arg91Gln | p.R91Q | P32119 | protein_coding | deleterious(0.03) | possibly_damaging(0.74) | TCGA-D5-7000-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PRDX2 | SNV | Missense_Mutation | c.38N>T | p.Pro13Leu | p.P13L | P32119 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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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