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Gene: PGA3 |
Gene summary for PGA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PGA3 | Gene ID | 643834 |
| Gene name | pepsinogen A3 | |
| Gene Alias | PGA3 | |
| Cytomap | 11q12.2 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | P0DJD8 |
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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 |
| 643834 | PGA3 | Pat01-B | Human | Stomach | GC | 3.08e-18 | -8.64e-01 | 0.5754 |
| 643834 | PGA3 | Pat02-B | Human | Stomach | GC | 6.74e-23 | -8.64e-01 | 0.0368 |
| 643834 | PGA3 | Pat03-B | Human | Stomach | GC | 2.91e-15 | -8.64e-01 | 0.3693 |
| 643834 | PGA3 | Pat04-B | Human | Stomach | GC | 5.62e-07 | -8.64e-01 | -0.1483 |
| 643834 | PGA3 | Pat05-B | Human | Stomach | GC | 6.89e-05 | -8.51e-01 | -0.0353 |
| 643834 | PGA3 | Pat06-B | Human | Stomach | GC | 3.32e-15 | -8.64e-01 | -0.1961 |
| 643834 | PGA3 | Pat07-B | Human | Stomach | GC | 4.90e-03 | -8.64e-01 | 0.0935 |
| 643834 | PGA3 | Pat08-B | Human | Stomach | GC | 2.08e-03 | -8.44e-01 | 0.0182 |
| 643834 | PGA3 | Pat09-B | Human | Stomach | GC | 9.23e-13 | -8.64e-01 | -0.0359 |
| 643834 | PGA3 | Pat10-B | Human | Stomach | GC | 7.37e-03 | -8.64e-01 | 0.084 |
| 643834 | PGA3 | Pat11-B | Human | Stomach | GC | 1.75e-05 | -8.64e-01 | -0.182 |
| 643834 | PGA3 | Pat12-B | Human | Stomach | GC | 1.52e-16 | -8.64e-01 | 0.0325 |
| 643834 | PGA3 | Pat13-B | Human | Stomach | GC | 3.57e-08 | -8.64e-01 | 0.0555 |
| 643834 | PGA3 | Pat15-B | Human | Stomach | GC | 8.26e-08 | -7.55e-01 | -0.0778 |
| 643834 | PGA3 | Pat16-B | Human | Stomach | GC | 6.74e-23 | -8.64e-01 | 0.1918 |
| 643834 | PGA3 | Pat17-B | Human | Stomach | GC | 1.34e-21 | -8.58e-01 | 0.3109 |
| 643834 | PGA3 | Pat18-B | Human | Stomach | GC | 2.15e-14 | -8.64e-01 | -0.0432 |
| 643834 | PGA3 | Pat19-B | Human | Stomach | GC | 2.00e-10 | -8.64e-01 | 0.0826 |
| 643834 | PGA3 | Pat22-B | Human | Stomach | GC | 3.41e-13 | -8.64e-01 | -0.1042 |
| 643834 | PGA3 | Pat24-B | Human | Stomach | GC | 1.76e-06 | -7.88e-01 | -0.1184 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:0007586 | Stomach | GC | digestion | 38/1159 | 137/18723 | 1.80e-15 | 1.22e-12 | 38 |
| GO:00075861 | Stomach | CAG with IM | digestion | 29/1050 | 137/18723 | 4.42e-10 | 6.93e-08 | 29 |
| GO:00075862 | Stomach | CSG | digestion | 25/1034 | 137/18723 | 1.15e-07 | 8.25e-06 | 25 |
| GO:00075863 | Stomach | CAG | digestion | 17/552 | 137/18723 | 6.00e-07 | 4.32e-05 | 17 |
| GO:00075864 | Stomach | WIM | digestion | 17/426 | 137/18723 | 1.48e-08 | 1.95e-06 | 17 |
| GO:00075865 | Stomach | SIM | digestion | 24/708 | 137/18723 | 3.20e-10 | 6.29e-08 | 24 |
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| 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 |
| PGA3 | SNV | Missense_Mutation | novel | c.865N>A | p.Pro289Thr | p.P289T | P0DJD8 | protein_coding | tolerated(0.28) | benign(0.056) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD |
| PGA3 | SNV | Missense_Mutation | novel | c.244N>G | p.Ile82Val | p.I82V | P0DJD8 | protein_coding | deleterious(0.04) | benign(0.369) | TCGA-AP-A054-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD |
| PGA3 | SNV | Missense_Mutation | novel | c.103N>T | p.Arg35Cys | p.R35C | P0DJD8 | protein_coding | deleterious(0.03) | benign(0.005) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.955G>T | p.Asp319Tyr | p.D319Y | P0DJD8 | protein_coding | deleterious(0.02) | probably_damaging(0.955) | TCGA-AP-A0LP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Hormone Therapy | megace | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.198G>T | p.Gln66His | p.Q66H | P0DJD8 | protein_coding | deleterious(0.04) | possibly_damaging(0.795) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.350N>A | p.Arg117His | p.R117H | P0DJD8 | protein_coding | deleterious(0.04) | benign(0.362) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.400N>C | p.Ser134Pro | p.S134P | P0DJD8 | protein_coding | deleterious(0.01) | probably_damaging(0.924) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.985T>C | p.Tyr329His | p.Y329H | P0DJD8 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| PGA3 | SNV | Missense_Mutation | novel | c.75N>T | p.Lys25Asn | p.K25N | P0DJD8 | protein_coding | tolerated(0.33) | benign(0.432) | TCGA-EO-A3AY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| PGA3 | SNV | Missense_Mutation | c.162C>G | p.Phe54Leu | p.F54L | P0DJD8 | protein_coding | tolerated(0.56) | benign(0.005) | TCGA-4B-A93V-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
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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 |
| 643834 | PGA3 | PROTEASE, DRUGGABLE GENOME, ENZYME | SUCRALFATE | SUCRALFATE | ||
| 643834 | PGA3 | PROTEASE, DRUGGABLE GENOME, ENZYME | SUCRALFATE | SUCRALFATE | ||
| 643834 | PGA3 | PROTEASE, DRUGGABLE GENOME, ENZYME | ECABET | ECABET |
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