|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: GPX1 |
Gene summary for GPX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | GPX1 | Gene ID | 2876 |
| Gene name | glutathione peroxidase 1 | |
| Gene Alias | GPXD | |
| Cytomap | 3p21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000302 | UniProtAcc | P07203 |
Top |
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 |
| 2876 | GPX1 | GSM4909281 | Human | Breast | IDC | 7.78e-22 | -3.72e-01 | 0.21 |
| 2876 | GPX1 | GSM4909282 | Human | Breast | IDC | 3.31e-22 | -3.72e-01 | -0.0288 |
| 2876 | GPX1 | GSM4909285 | Human | Breast | IDC | 1.82e-21 | -3.72e-01 | 0.21 |
| 2876 | GPX1 | GSM4909286 | Human | Breast | IDC | 1.82e-21 | -3.72e-01 | 0.1081 |
| 2876 | GPX1 | GSM4909287 | Human | Breast | IDC | 3.56e-19 | -3.72e-01 | 0.2057 |
| 2876 | GPX1 | GSM4909288 | Human | Breast | IDC | 3.47e-04 | -3.72e-01 | 0.0988 |
| 2876 | GPX1 | GSM4909289 | Human | Breast | IDC | 9.03e-03 | -3.72e-01 | 0.1064 |
| 2876 | GPX1 | GSM4909290 | Human | Breast | IDC | 1.25e-13 | -3.72e-01 | 0.2096 |
| 2876 | GPX1 | GSM4909291 | Human | Breast | IDC | 5.65e-11 | -3.72e-01 | 0.1753 |
| 2876 | GPX1 | GSM4909293 | Human | Breast | IDC | 7.78e-22 | -3.72e-01 | 0.1581 |
| 2876 | GPX1 | GSM4909294 | Human | Breast | IDC | 3.31e-22 | -3.72e-01 | 0.2022 |
| 2876 | GPX1 | GSM4909295 | Human | Breast | IDC | 1.54e-08 | -3.72e-01 | 0.0898 |
| 2876 | GPX1 | GSM4909296 | Human | Breast | IDC | 7.78e-22 | -3.72e-01 | 0.1524 |
| 2876 | GPX1 | GSM4909297 | Human | Breast | IDC | 1.06e-23 | -3.72e-01 | 0.1517 |
| 2876 | GPX1 | GSM4909298 | Human | Breast | IDC | 1.82e-21 | -3.72e-01 | 0.1551 |
| 2876 | GPX1 | GSM4909299 | Human | Breast | IDC | 3.31e-22 | -3.72e-01 | 0.035 |
| 2876 | GPX1 | GSM4909300 | Human | Breast | IDC | 1.73e-07 | -3.72e-01 | 0.0334 |
| 2876 | GPX1 | GSM4909301 | Human | Breast | IDC | 2.52e-23 | -3.72e-01 | 0.1577 |
| 2876 | GPX1 | GSM4909302 | Human | Breast | IDC | 6.78e-19 | -3.72e-01 | 0.1545 |
| 2876 | GPX1 | GSM4909303 | Human | Breast | IDC | 7.99e-05 | -3.72e-01 | 0.0438 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 | ||
| 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 | ||
| 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 |
| ∗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. |
Top |
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:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
| GO:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
| GO:20012429 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway | 41/1080 | 164/18723 | 6.48e-16 | 2.31e-13 | 41 |
| GO:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
| GO:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
| GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
| GO:20001169 | Breast | Precancer | regulation of cysteine-type endopeptidase activity | 43/1080 | 235/18723 | 1.30e-11 | 1.83e-09 | 43 |
| GO:00432819 | Breast | Precancer | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 40/1080 | 209/18723 | 1.59e-11 | 2.07e-09 | 40 |
| GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
| GO:20012349 | Breast | Precancer | negative regulation of apoptotic signaling pathway | 39/1080 | 224/18723 | 5.35e-10 | 4.77e-08 | 39 |
| GO:00003029 | Breast | Precancer | response to reactive oxygen species | 38/1080 | 222/18723 | 1.47e-09 | 1.23e-07 | 38 |
| GO:00458619 | Breast | Precancer | negative regulation of proteolysis | 50/1080 | 351/18723 | 2.99e-09 | 2.39e-07 | 50 |
| GO:20012439 | Breast | Precancer | negative regulation of intrinsic apoptotic signaling pathway | 23/1080 | 98/18723 | 5.82e-09 | 4.45e-07 | 23 |
| GO:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
| GO:00514029 | Breast | Precancer | neuron apoptotic process | 38/1080 | 246/18723 | 2.68e-08 | 1.75e-06 | 38 |
| GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
| GO:00444039 | Breast | Precancer | biological process involved in symbiotic interaction | 42/1080 | 290/18723 | 3.40e-08 | 2.11e-06 | 42 |
| GO:00086378 | Breast | Precancer | apoptotic mitochondrial changes | 23/1080 | 107/18723 | 3.44e-08 | 2.12e-06 | 23 |
| GO:00513468 | Breast | Precancer | negative regulation of hydrolase activity | 50/1080 | 379/18723 | 3.85e-08 | 2.34e-06 | 50 |
| GO:00104668 | Breast | Precancer | negative regulation of peptidase activity | 38/1080 | 262/18723 | 1.46e-07 | 7.82e-06 | 38 |
| 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 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa050165 | Colorectum | MSS | Huntington disease | 141/1875 | 306/8465 | 2.90e-21 | 1.62e-19 | 9.92e-20 | 141 |
| hsa050225 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
| hsa050145 | Colorectum | MSS | Amyotrophic lateral sclerosis | 156/1875 | 364/8465 | 1.43e-19 | 4.62e-18 | 2.83e-18 | 156 |
| hsa004803 | Colorectum | MSS | Glutathione metabolism | 22/1875 | 57/8465 | 3.58e-03 | 1.64e-02 | 1.01e-02 | 22 |
| hsa050146 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
| hsa050166 | Colorectum | MSI-H | Huntington disease | 83/797 | 306/8465 | 7.06e-20 | 3.81e-18 | 3.20e-18 | 83 |
| hsa050226 | Colorectum | MSI-H | Pathways of neurodegeneration - multiple diseases | 107/797 | 476/8465 | 1.24e-18 | 5.72e-17 | 4.80e-17 | 107 |
| hsa050147 | Colorectum | MSI-H | Amyotrophic lateral sclerosis | 95/797 | 364/8465 | 2.31e-21 | 1.50e-19 | 1.26e-19 | 95 |
| hsa050167 | Colorectum | MSI-H | Huntington disease | 83/797 | 306/8465 | 7.06e-20 | 3.81e-18 | 3.20e-18 | 83 |
| hsa050227 | Colorectum | MSI-H | Pathways of neurodegeneration - multiple diseases | 107/797 | 476/8465 | 1.24e-18 | 5.72e-17 | 4.80e-17 | 107 |
| hsa0501630 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa0501430 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
| hsa0502230 | Esophagus | HGIN | Pathways of neurodegeneration - multiple diseases | 153/1383 | 476/8465 | 1.22e-18 | 4.41e-17 | 3.50e-17 | 153 |
| hsa05016113 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa05014113 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
| hsa05022113 | Esophagus | HGIN | Pathways of neurodegeneration - multiple diseases | 153/1383 | 476/8465 | 1.22e-18 | 4.41e-17 | 3.50e-17 | 153 |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| hsa05022210 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
| hsa0048018 | Esophagus | ESCC | Glutathione metabolism | 44/4205 | 57/8465 | 1.81e-05 | 9.03e-05 | 4.63e-05 | 44 |
| Page: 1 2 3 4 5 6 7 8 9 |
Top |
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 |
Top |
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 |
Top |
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 |
| GPX1 | SNV | Missense_Mutation | novel | c.475N>A | p.Asp159Asn | p.D159N | P07203 | protein_coding | deleterious(0.04) | possibly_damaging(0.675) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| GPX1 | SNV | Missense_Mutation | c.489C>G | p.Asn163Lys | p.N163K | P07203 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3976-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | CR | |
| GPX1 | SNV | Missense_Mutation | c.109N>A | p.Gly37Ser | p.G37S | P07203 | protein_coding | deleterious(0.01) | probably_damaging(0.945) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GPX1 | insertion | Frame_Shift_Ins | novel | c.364_365insG | p.Ala122GlyfsTer? | p.A122Gfs*? | P07203 | protein_coding | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| GPX1 | SNV | Missense_Mutation | novel | c.264G>T | p.Lys88Asn | p.K88N | P07203 | protein_coding | tolerated(0.43) | benign(0.027) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD |
| GPX1 | SNV | Missense_Mutation | novel | c.493N>A | p.Glu165Lys | p.E165K | P07203 | protein_coding | deleterious(0.02) | probably_damaging(0.941) | TCGA-DD-A114-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| GPX1 | SNV | Missense_Mutation | c.110G>A | p.Gly37Asp | p.G37D | P07203 | protein_coding | tolerated(0.12) | benign(0.355) | TCGA-DD-A73B-01 | Liver | liver hepatocellular carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| GPX1 | SNV | Missense_Mutation | rs755209006 | c.524N>T | p.Pro175Leu | p.P175L | P07203 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-50-7109-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| GPX1 | SNV | Missense_Mutation | c.415G>A | p.Asp139Asn | p.D139N | P07203 | protein_coding | tolerated(0.07) | benign(0.193) | TCGA-55-7727-01 | Lung | lung adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| GPX1 | SNV | Missense_Mutation | c.436G>T | p.Asp146Tyr | p.D146Y | P07203 | protein_coding | deleterious(0) | probably_damaging(0.928) | TCGA-55-A4DF-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 |
Top |
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 |
| 2876 | GPX1 | DRUGGABLE GENOME, PROTEASE INHIBITOR | GP-120 | 16871233 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |