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Gene: PSMA3 |
Gene summary for PSMA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMA3 | Gene ID | 5684 |
| Gene name | proteasome 20S subunit alpha 3 | |
| Gene Alias | HC8 | |
| Cytomap | 14q23.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | A0A140VK43 |
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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 |
| 5684 | PSMA3 | GSM4909285 | Human | Breast | IDC | 4.26e-05 | 3.05e-01 | 0.21 |
| 5684 | PSMA3 | GSM4909286 | Human | Breast | IDC | 4.26e-04 | -2.43e-01 | 0.1081 |
| 5684 | PSMA3 | GSM4909291 | Human | Breast | IDC | 1.20e-03 | -3.78e-01 | 0.1753 |
| 5684 | PSMA3 | GSM4909296 | Human | Breast | IDC | 1.98e-07 | 5.30e-03 | 0.1524 |
| 5684 | PSMA3 | GSM4909297 | Human | Breast | IDC | 3.01e-12 | -2.64e-01 | 0.1517 |
| 5684 | PSMA3 | GSM4909301 | Human | Breast | IDC | 7.20e-14 | -3.87e-01 | 0.1577 |
| 5684 | PSMA3 | GSM4909302 | Human | Breast | IDC | 8.01e-03 | -2.97e-01 | 0.1545 |
| 5684 | PSMA3 | GSM4909311 | Human | Breast | IDC | 1.47e-30 | -4.09e-01 | 0.1534 |
| 5684 | PSMA3 | GSM4909312 | Human | Breast | IDC | 1.69e-12 | -2.18e-01 | 0.1552 |
| 5684 | PSMA3 | GSM4909313 | Human | Breast | IDC | 1.07e-04 | -3.38e-01 | 0.0391 |
| 5684 | PSMA3 | GSM4909319 | Human | Breast | IDC | 1.21e-35 | -3.58e-01 | 0.1563 |
| 5684 | PSMA3 | GSM4909320 | Human | Breast | IDC | 6.75e-09 | -4.26e-01 | 0.1575 |
| 5684 | PSMA3 | GSM4909321 | Human | Breast | IDC | 2.99e-13 | -2.44e-01 | 0.1559 |
| 5684 | PSMA3 | brca1 | Human | Breast | Precancer | 1.33e-23 | 5.98e-01 | -0.0338 |
| 5684 | PSMA3 | brca2 | Human | Breast | Precancer | 1.51e-20 | 5.22e-01 | -0.024 |
| 5684 | PSMA3 | brca3 | Human | Breast | Precancer | 8.60e-07 | 3.43e-01 | -0.0263 |
| 5684 | PSMA3 | NCCBC14 | Human | Breast | DCIS | 7.96e-07 | 4.23e-02 | 0.2021 |
| 5684 | PSMA3 | NCCBC5 | Human | Breast | DCIS | 4.40e-08 | 5.44e-02 | 0.2046 |
| 5684 | PSMA3 | P1 | Human | Breast | IDC | 1.66e-16 | -2.21e-01 | 0.1527 |
| 5684 | PSMA3 | P2 | Human | Breast | IDC | 4.98e-03 | 2.60e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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: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:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:005254714 | Breast | IDC | regulation of peptidase activity | 96/1434 | 461/18723 | 7.58e-20 | 6.15e-17 | 96 |
| GO:005254814 | Breast | IDC | regulation of endopeptidase activity | 88/1434 | 432/18723 | 1.20e-17 | 4.85e-15 | 88 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:005254723 | Breast | DCIS | regulation of peptidase activity | 88/1390 | 461/18723 | 1.18e-16 | 4.78e-14 | 88 |
| GO:005254823 | Breast | DCIS | regulation of endopeptidase activity | 83/1390 | 432/18723 | 6.07e-16 | 2.15e-13 | 83 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:00104982 | Colorectum | MSS | proteasomal protein catabolic process | 157/3467 | 490/18723 | 2.39e-13 | 5.25e-11 | 157 |
| GO:00525472 | Colorectum | MSS | regulation of peptidase activity | 130/3467 | 461/18723 | 1.81e-07 | 8.13e-06 | 130 |
| GO:00525482 | Colorectum | MSS | regulation of endopeptidase activity | 117/3467 | 432/18723 | 6.25e-06 | 1.65e-04 | 117 |
| GO:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
| GO:00525473 | Colorectum | MSI-H | regulation of peptidase activity | 66/1319 | 461/18723 | 2.63e-08 | 2.81e-06 | 66 |
| GO:00525483 | Colorectum | MSI-H | regulation of endopeptidase activity | 60/1319 | 432/18723 | 3.29e-07 | 2.57e-05 | 60 |
| GO:00104984 | Colorectum | FAP | proteasomal protein catabolic process | 110/2622 | 490/18723 | 2.12e-07 | 1.26e-05 | 110 |
| GO:00525474 | Colorectum | FAP | regulation of peptidase activity | 86/2622 | 461/18723 | 2.98e-03 | 2.27e-02 | 86 |
| GO:00525484 | Colorectum | FAP | regulation of endopeptidase activity | 79/2622 | 432/18723 | 7.15e-03 | 4.36e-02 | 79 |
| GO:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
| GO:005254726 | Esophagus | HGIN | regulation of peptidase activity | 102/2587 | 461/18723 | 6.29e-07 | 2.72e-05 | 102 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501218 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502016 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| 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 |
| hsa0305010 | Breast | Precancer | Proteasome | 25/684 | 46/8465 | 4.35e-16 | 9.81e-15 | 7.52e-15 | 25 |
| hsa0501714 | Breast | Precancer | Spinocerebellar ataxia | 29/684 | 143/8465 | 2.79e-06 | 3.83e-05 | 2.94e-05 | 29 |
| hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502017 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| 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 |
| hsa0305013 | Breast | Precancer | Proteasome | 25/684 | 46/8465 | 4.35e-16 | 9.81e-15 | 7.52e-15 | 25 |
| hsa0501715 | Breast | Precancer | Spinocerebellar ataxia | 29/684 | 143/8465 | 2.79e-06 | 3.83e-05 | 2.94e-05 | 29 |
| hsa0501224 | Breast | IDC | Parkinson disease | 107/867 | 266/8465 | 2.57e-39 | 8.36e-37 | 6.26e-37 | 107 |
| hsa0502023 | Breast | IDC | Prion disease | 102/867 | 273/8465 | 3.70e-34 | 4.01e-32 | 3.00e-32 | 102 |
| hsa0501623 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
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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 |
| PSMA3 | SNV | Missense_Mutation | c.344N>C | p.Arg115Thr | p.R115T | P25788 | protein_coding | deleterious(0) | possibly_damaging(0.757) | TCGA-A2-A0YH-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| PSMA3 | SNV | Missense_Mutation | c.178N>A | p.Glu60Lys | p.E60K | P25788 | protein_coding | tolerated(0.18) | probably_damaging(0.984) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| PSMA3 | SNV | Missense_Mutation | c.675N>A | p.His225Gln | p.H225Q | P25788 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-D8-A1X6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |
| PSMA3 | SNV | Missense_Mutation | novel | c.748T>C | p.Ser250Pro | p.S250P | P25788 | protein_coding | tolerated(0.13) | benign(0.307) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA3 | SNV | Missense_Mutation | rs749644838 | c.214N>T | p.Arg72Trp | p.R72W | P25788 | protein_coding | deleterious(0.01) | benign(0.082) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA3 | SNV | Missense_Mutation | novel | c.116G>T | p.Gly39Val | p.G39V | P25788 | protein_coding | deleterious(0.02) | benign(0.419) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PSMA3 | SNV | Missense_Mutation | c.122N>T | p.Arg41Ile | p.R41I | P25788 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AF-2693-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PSMA3 | SNV | Missense_Mutation | c.344G>T | p.Arg115Ile | p.R115I | P25788 | protein_coding | deleterious(0) | probably_damaging(0.96) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PSMA3 | SNV | Missense_Mutation | c.610G>A | p.Glu204Lys | p.E204K | P25788 | protein_coding | deleterious(0) | benign(0.182) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PSMA3 | SNV | Missense_Mutation | novel | c.340G>C | p.Asp114His | p.D114H | P25788 | protein_coding | deleterious(0.01) | benign(0.162) | TCGA-AJ-A2QM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | CR |
| Page: 1 2 3 |
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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 |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL371405 | MARIZOMIB | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5684 | PSMA3 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL451887 | CARFILZOMIB |
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