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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 |
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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 |
| 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. |
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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:0010639110 | Esophagus | ESCC | negative regulation of organelle organization | 215/8552 | 348/18723 | 8.20e-10 | 2.01e-08 | 215 |
| GO:0042542111 | Esophagus | ESCC | response to hydrogen peroxide | 102/8552 | 146/18723 | 2.64e-09 | 5.81e-08 | 102 |
| GO:0070997111 | Esophagus | ESCC | neuron death | 216/8552 | 361/18723 | 3.49e-08 | 6.45e-07 | 216 |
| GO:0052548111 | Esophagus | ESCC | regulation of endopeptidase activity | 253/8552 | 432/18723 | 3.68e-08 | 6.78e-07 | 253 |
| GO:0008631110 | Esophagus | ESCC | intrinsic apoptotic signaling pathway in response to oxidative stress | 38/8552 | 45/18723 | 8.42e-08 | 1.43e-06 | 38 |
| GO:000183619 | Esophagus | ESCC | release of cytochrome c from mitochondria | 47/8552 | 59/18723 | 9.02e-08 | 1.51e-06 | 47 |
| GO:2000117110 | Esophagus | ESCC | negative regulation of cysteine-type endopeptidase activity | 63/8552 | 86/18723 | 1.84e-07 | 2.88e-06 | 63 |
| GO:00400295 | Esophagus | ESCC | regulation of gene expression, epigenetic | 74/8552 | 105/18723 | 2.24e-07 | 3.42e-06 | 74 |
| GO:0043154110 | Esophagus | ESCC | negative regulation of cysteine-type endopeptidase activity involved in apoptotic process | 58/8552 | 78/18723 | 2.38e-07 | 3.61e-06 | 58 |
| GO:00067906 | Esophagus | ESCC | sulfur compound metabolic process | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
| GO:2001237111 | Esophagus | ESCC | negative regulation of extrinsic apoptotic signaling pathway | 69/8552 | 97/18723 | 3.23e-07 | 4.55e-06 | 69 |
| GO:004206027 | Esophagus | ESCC | wound healing | 243/8552 | 422/18723 | 4.62e-07 | 6.25e-06 | 243 |
| GO:000206420 | Esophagus | ESCC | epithelial cell development | 136/8552 | 220/18723 | 9.50e-07 | 1.21e-05 | 136 |
| GO:000862519 | Esophagus | ESCC | extrinsic apoptotic signaling pathway via death domain receptors | 59/8552 | 82/18723 | 1.23e-06 | 1.52e-05 | 59 |
| GO:009019914 | Esophagus | ESCC | regulation of release of cytochrome c from mitochondria | 38/8552 | 48/18723 | 2.11e-06 | 2.43e-05 | 38 |
| GO:0051402110 | Esophagus | ESCC | neuron apoptotic process | 148/8552 | 246/18723 | 3.08e-06 | 3.47e-05 | 148 |
| GO:003109910 | Esophagus | ESCC | regeneration | 122/8552 | 198/18723 | 4.26e-06 | 4.57e-05 | 122 |
| GO:004545419 | Esophagus | ESCC | cell redox homeostasis | 29/8552 | 35/18723 | 6.61e-06 | 6.75e-05 | 29 |
| GO:000941611 | Esophagus | ESCC | response to light stimulus | 183/8552 | 320/18723 | 2.03e-05 | 1.76e-04 | 183 |
| GO:001033215 | Esophagus | ESCC | response to gamma radiation | 41/8552 | 56/18723 | 2.64e-05 | 2.21e-04 | 41 |
| 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 |
| hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0501416 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0048010 | Breast | Precancer | Glutathione metabolism | 12/684 | 57/8465 | 1.68e-03 | 1.08e-02 | 8.30e-03 | 12 |
| hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0501417 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0048013 | Breast | Precancer | Glutathione metabolism | 12/684 | 57/8465 | 1.68e-03 | 1.08e-02 | 8.30e-03 | 12 |
| hsa0501623 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0501423 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
| hsa0502223 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0048023 | Breast | IDC | Glutathione metabolism | 13/867 | 57/8465 | 4.25e-03 | 2.56e-02 | 1.91e-02 | 13 |
| hsa0501633 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0501433 | Breast | IDC | Amyotrophic lateral sclerosis | 102/867 | 364/8465 | 1.29e-22 | 5.22e-21 | 3.91e-21 | 102 |
| hsa0502233 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0048033 | Breast | IDC | Glutathione metabolism | 13/867 | 57/8465 | 4.25e-03 | 2.56e-02 | 1.91e-02 | 13 |
| hsa0501643 | Breast | DCIS | Huntington disease | 101/846 | 306/8465 | 1.54e-29 | 1.24e-27 | 9.13e-28 | 101 |
| hsa0501443 | Breast | DCIS | Amyotrophic lateral sclerosis | 101/846 | 364/8465 | 7.14e-23 | 2.88e-21 | 2.12e-21 | 101 |
| hsa0502243 | Breast | DCIS | Pathways of neurodegeneration - multiple diseases | 114/846 | 476/8465 | 4.74e-20 | 1.53e-18 | 1.13e-18 | 114 |
| hsa0501653 | Breast | DCIS | Huntington disease | 101/846 | 306/8465 | 1.54e-29 | 1.24e-27 | 9.13e-28 | 101 |
| Page: 1 2 3 4 5 6 7 8 9 |
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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 |
| 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 |
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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 |
| 2876 | GPX1 | DRUGGABLE GENOME, PROTEASE INHIBITOR | GP-120 | 16871233 |
| Page: 1 |
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