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Gene: PSMA1 |
Gene summary for PSMA1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMA1 | Gene ID | 5682 |
| Gene name | proteasome 20S subunit alpha 1 | |
| Gene Alias | HC2 | |
| Cytomap | 11p15.2 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | B4E0X6 |
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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 |
| 5682 | PSMA1 | GSM4909286 | Human | Breast | IDC | 1.20e-02 | -2.12e-01 | 0.1081 |
| 5682 | PSMA1 | GSM4909294 | Human | Breast | IDC | 1.63e-02 | -6.13e-02 | 0.2022 |
| 5682 | PSMA1 | GSM4909296 | Human | Breast | IDC | 1.04e-10 | -2.21e-01 | 0.1524 |
| 5682 | PSMA1 | GSM4909297 | Human | Breast | IDC | 1.57e-16 | -2.36e-01 | 0.1517 |
| 5682 | PSMA1 | GSM4909301 | Human | Breast | IDC | 1.93e-18 | -4.73e-01 | 0.1577 |
| 5682 | PSMA1 | GSM4909302 | Human | Breast | IDC | 2.83e-03 | -3.77e-01 | 0.1545 |
| 5682 | PSMA1 | GSM4909311 | Human | Breast | IDC | 1.27e-36 | -5.13e-01 | 0.1534 |
| 5682 | PSMA1 | GSM4909312 | Human | Breast | IDC | 1.70e-15 | -6.31e-02 | 0.1552 |
| 5682 | PSMA1 | GSM4909316 | Human | Breast | IDC | 7.24e-05 | 2.27e-01 | 0.21 |
| 5682 | PSMA1 | GSM4909319 | Human | Breast | IDC | 4.61e-44 | -4.87e-01 | 0.1563 |
| 5682 | PSMA1 | GSM4909320 | Human | Breast | IDC | 9.61e-08 | -5.53e-01 | 0.1575 |
| 5682 | PSMA1 | GSM4909321 | Human | Breast | IDC | 1.75e-16 | -1.89e-01 | 0.1559 |
| 5682 | PSMA1 | brca1 | Human | Breast | Precancer | 2.11e-16 | 5.38e-01 | -0.0338 |
| 5682 | PSMA1 | brca2 | Human | Breast | Precancer | 8.06e-21 | 4.62e-01 | -0.024 |
| 5682 | PSMA1 | brca3 | Human | Breast | Precancer | 6.07e-16 | 4.08e-01 | -0.0263 |
| 5682 | PSMA1 | NCCBC14 | Human | Breast | DCIS | 3.58e-09 | 7.22e-03 | 0.2021 |
| 5682 | PSMA1 | NCCBC5 | Human | Breast | DCIS | 9.92e-12 | -1.09e-01 | 0.2046 |
| 5682 | PSMA1 | P1 | Human | Breast | IDC | 2.12e-13 | -3.98e-01 | 0.1527 |
| 5682 | PSMA1 | DCIS2 | Human | Breast | DCIS | 4.50e-63 | 3.40e-02 | 0.0085 |
| 5682 | PSMA1 | CA_HPV_1 | Human | Cervix | CC | 9.28e-04 | -2.16e-02 | 0.0264 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:001049810 | Cervix | CC | proteasomal protein catabolic process | 111/2311 | 490/18723 | 8.98e-11 | 1.58e-08 | 111 |
| GO:001049816 | Endometrium | AEH | proteasomal protein catabolic process | 108/2100 | 490/18723 | 2.73e-12 | 4.67e-10 | 108 |
| GO:001049817 | Endometrium | EEC | proteasomal protein catabolic process | 112/2168 | 490/18723 | 6.99e-13 | 1.40e-10 | 112 |
| GO:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
| GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
| GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:0010498110 | Oral cavity | LP | proteasomal protein catabolic process | 224/4623 | 490/18723 | 9.57e-25 | 4.00e-22 | 224 |
| GO:001049831 | Oral cavity | NEOLP | proteasomal protein catabolic process | 103/2005 | 490/18723 | 1.08e-11 | 1.65e-09 | 103 |
| GO:001049818 | Prostate | BPH | proteasomal protein catabolic process | 153/3107 | 490/18723 | 4.13e-16 | 7.51e-14 | 153 |
| GO:001049819 | Prostate | Tumor | proteasomal protein catabolic process | 158/3246 | 490/18723 | 3.05e-16 | 6.76e-14 | 158 |
| GO:001049828 | Skin | cSCC | proteasomal protein catabolic process | 243/4864 | 490/18723 | 7.85e-30 | 4.10e-27 | 243 |
| GO:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
| GO:001049832 | Thyroid | ATC | proteasomal protein catabolic process | 309/6293 | 490/18723 | 1.78e-41 | 1.13e-37 | 309 |
| Page: 1 |
| 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 13 |
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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 |
| PSMA1 | SNV | Missense_Mutation | c.198N>T | p.Gln66His | p.Q66H | P25786 | protein_coding | deleterious(0.01) | possibly_damaging(0.52) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PSMA1 | SNV | Missense_Mutation | rs751551757 | c.316G>A | p.Asp106Asn | p.D106N | P25786 | protein_coding | tolerated(0.6) | benign(0.005) | TCGA-AC-A2FO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | chemo | CR |
| PSMA1 | SNV | Missense_Mutation | novel | c.476A>G | p.Tyr159Cys | p.Y159C | P25786 | protein_coding | tolerated(0.12) | probably_damaging(0.971) | TCGA-VS-A950-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
| PSMA1 | SNV | Missense_Mutation | novel | c.26N>A | p.Arg9Gln | p.R9Q | P25786 | protein_coding | deleterious(0) | probably_damaging(0.969) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA1 | SNV | Missense_Mutation | c.284N>T | p.Arg95Leu | p.R95L | P25786 | protein_coding | deleterious(0) | possibly_damaging(0.896) | TCGA-G4-6317-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | fluorouracil | PD | |
| PSMA1 | SNV | Missense_Mutation | rs776935096 | c.242C>T | p.Ala81Val | p.A81V | P25786 | protein_coding | deleterious(0) | probably_damaging(0.924) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| PSMA1 | SNV | Missense_Mutation | novel | c.233T>A | p.Ile78Asn | p.I78N | P25786 | protein_coding | deleterious(0) | possibly_damaging(0.89) | TCGA-AX-A063-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA1 | SNV | Missense_Mutation | novel | c.154N>G | p.Leu52Val | p.L52V | P25786 | protein_coding | deleterious(0.02) | benign(0.268) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| PSMA1 | SNV | Missense_Mutation | novel | c.91N>C | p.Ala31Pro | p.A31P | P25786 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PSMA1 | SNV | Missense_Mutation | novel | c.278N>G | p.Phe93Cys | p.F93C | P25786 | protein_coding | deleterious(0) | probably_damaging(0.935) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL371405 | MARIZOMIB | |
| 5682 | PSMA1 | PROTEASE, DRUGGABLE GENOME | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE |
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