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Gene: PSMA2 |
Gene summary for PSMA2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMA2 | Gene ID | 5683 |
| Gene name | proteasome 20S subunit alpha 2 | |
| Gene Alias | HC3 | |
| Cytomap | 7p14.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | A0A024RA52 |
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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 |
| 5683 | PSMA2 | CA_HPV_1 | Human | Cervix | CC | 2.22e-05 | -3.86e-05 | 0.0264 |
| 5683 | PSMA2 | CA_HPV_3 | Human | Cervix | CC | 2.30e-02 | 7.95e-02 | 0.0414 |
| 5683 | PSMA2 | CCI_1 | Human | Cervix | CC | 4.28e-09 | -5.82e-01 | 0.528 |
| 5683 | PSMA2 | CCI_2 | Human | Cervix | CC | 2.64e-08 | -5.82e-01 | 0.5249 |
| 5683 | PSMA2 | CCI_3 | Human | Cervix | CC | 2.82e-12 | -5.82e-01 | 0.516 |
| 5683 | PSMA2 | CCII_1 | Human | Cervix | CC | 3.87e-17 | -5.82e-01 | 0.3249 |
| 5683 | PSMA2 | sample3 | Human | Cervix | CC | 6.07e-09 | 3.48e-01 | 0.1387 |
| 5683 | PSMA2 | L1 | Human | Cervix | CC | 6.21e-03 | -1.33e-02 | 0.0802 |
| 5683 | PSMA2 | T3 | Human | Cervix | CC | 1.45e-06 | 3.41e-01 | 0.1389 |
| 5683 | PSMA2 | AEH-subject1 | Human | Endometrium | AEH | 2.71e-05 | -2.03e-01 | -0.3059 |
| 5683 | PSMA2 | AEH-subject2 | Human | Endometrium | AEH | 3.09e-06 | -1.49e-01 | -0.2525 |
| 5683 | PSMA2 | AEH-subject3 | Human | Endometrium | AEH | 1.51e-08 | -1.28e-01 | -0.2576 |
| 5683 | PSMA2 | EEC-subject1 | Human | Endometrium | EEC | 4.88e-05 | -1.65e-01 | -0.2682 |
| 5683 | PSMA2 | EEC-subject2 | Human | Endometrium | EEC | 2.35e-06 | -2.37e-01 | -0.2607 |
| 5683 | PSMA2 | EEC-subject3 | Human | Endometrium | EEC | 2.25e-29 | -2.39e-01 | -0.2525 |
| 5683 | PSMA2 | EEC-subject4 | Human | Endometrium | EEC | 2.69e-05 | 6.89e-02 | -0.2571 |
| 5683 | PSMA2 | EEC-subject5 | Human | Endometrium | EEC | 8.66e-03 | -2.60e-03 | -0.249 |
| 5683 | PSMA2 | GSM5276934 | Human | Endometrium | EEC | 1.06e-03 | -2.20e-01 | -0.0913 |
| 5683 | PSMA2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 4.03e-19 | -1.55e-01 | -0.1869 |
| 5683 | PSMA2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 2.11e-19 | -1.66e-01 | -0.1875 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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:001049810 | Cervix | CC | proteasomal protein catabolic process | 111/2311 | 490/18723 | 8.98e-11 | 1.58e-08 | 111 |
| GO:004316110 | Cervix | CC | proteasome-mediated ubiquitin-dependent protein catabolic process | 91/2311 | 412/18723 | 1.65e-08 | 1.25e-06 | 91 |
| GO:00096158 | Cervix | CC | response to virus | 73/2311 | 367/18723 | 2.22e-05 | 3.95e-04 | 73 |
| GO:001049816 | Endometrium | AEH | proteasomal protein catabolic process | 108/2100 | 490/18723 | 2.73e-12 | 4.67e-10 | 108 |
| GO:004316116 | Endometrium | AEH | proteasome-mediated ubiquitin-dependent protein catabolic process | 88/2100 | 412/18723 | 1.54e-09 | 1.36e-07 | 88 |
| GO:00096159 | Endometrium | AEH | response to virus | 63/2100 | 367/18723 | 3.81e-04 | 4.10e-03 | 63 |
| GO:001049817 | Endometrium | EEC | proteasomal protein catabolic process | 112/2168 | 490/18723 | 6.99e-13 | 1.40e-10 | 112 |
| GO:004316117 | Endometrium | EEC | proteasome-mediated ubiquitin-dependent protein catabolic process | 92/2168 | 412/18723 | 3.01e-10 | 3.23e-08 | 92 |
| GO:000961513 | Endometrium | EEC | response to virus | 66/2168 | 367/18723 | 1.78e-04 | 2.20e-03 | 66 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
| GO:004316112 | Liver | Cirrhotic | proteasome-mediated ubiquitin-dependent protein catabolic process | 184/4634 | 412/18723 | 4.52e-19 | 8.85e-17 | 184 |
| GO:00096155 | Liver | Cirrhotic | response to virus | 126/4634 | 367/18723 | 2.10e-05 | 2.77e-04 | 126 |
| GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
| GO:004316122 | Liver | HCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 299/7958 | 412/18723 | 7.82e-36 | 8.27e-33 | 299 |
| GO:000961511 | Liver | HCC | response to virus | 210/7958 | 367/18723 | 7.32e-09 | 1.86e-07 | 210 |
| GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:004316120 | Oral cavity | OSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 285/7305 | 412/18723 | 5.68e-36 | 5.99e-33 | 285 |
| Page: 1 2 3 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501220 | Cervix | CC | Parkinson disease | 102/1267 | 266/8465 | 1.81e-21 | 1.47e-19 | 8.66e-20 | 102 |
| hsa0502018 | Cervix | CC | Prion disease | 98/1267 | 273/8465 | 2.64e-18 | 1.42e-16 | 8.42e-17 | 98 |
| hsa0501018 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
| hsa0501618 | Cervix | CC | Huntington disease | 94/1267 | 306/8465 | 8.49e-13 | 3.06e-11 | 1.81e-11 | 94 |
| hsa0502218 | Cervix | CC | Pathways of neurodegeneration - multiple diseases | 128/1267 | 476/8465 | 2.87e-12 | 9.29e-11 | 5.50e-11 | 128 |
| hsa0501418 | Cervix | CC | Amyotrophic lateral sclerosis | 103/1267 | 364/8465 | 1.79e-11 | 4.47e-10 | 2.64e-10 | 103 |
| hsa0305014 | Cervix | CC | Proteasome | 16/1267 | 46/8465 | 6.69e-04 | 3.09e-03 | 1.83e-03 | 16 |
| hsa0501716 | Cervix | CC | Spinocerebellar ataxia | 35/1267 | 143/8465 | 1.77e-03 | 7.21e-03 | 4.26e-03 | 35 |
| hsa05012110 | Cervix | CC | Parkinson disease | 102/1267 | 266/8465 | 1.81e-21 | 1.47e-19 | 8.66e-20 | 102 |
| hsa0502019 | Cervix | CC | Prion disease | 98/1267 | 273/8465 | 2.64e-18 | 1.42e-16 | 8.42e-17 | 98 |
| hsa0501019 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
| hsa0501619 | Cervix | CC | Huntington disease | 94/1267 | 306/8465 | 8.49e-13 | 3.06e-11 | 1.81e-11 | 94 |
| hsa0502219 | Cervix | CC | Pathways of neurodegeneration - multiple diseases | 128/1267 | 476/8465 | 2.87e-12 | 9.29e-11 | 5.50e-11 | 128 |
| hsa0501419 | Cervix | CC | Amyotrophic lateral sclerosis | 103/1267 | 364/8465 | 1.79e-11 | 4.47e-10 | 2.64e-10 | 103 |
| hsa0305015 | Cervix | CC | Proteasome | 16/1267 | 46/8465 | 6.69e-04 | 3.09e-03 | 1.83e-03 | 16 |
| hsa0501717 | Cervix | CC | Spinocerebellar ataxia | 35/1267 | 143/8465 | 1.77e-03 | 7.21e-03 | 4.26e-03 | 35 |
| hsa0501226 | Endometrium | AEH | Parkinson disease | 115/1197 | 266/8465 | 6.24e-32 | 1.01e-29 | 7.42e-30 | 115 |
| hsa0502020 | Endometrium | AEH | Prion disease | 110/1197 | 273/8465 | 2.39e-27 | 2.44e-25 | 1.78e-25 | 110 |
| hsa0501620 | Endometrium | AEH | Huntington disease | 118/1197 | 306/8465 | 3.00e-27 | 2.44e-25 | 1.78e-25 | 118 |
| hsa0501420 | Endometrium | AEH | Amyotrophic lateral sclerosis | 123/1197 | 364/8465 | 2.17e-22 | 7.82e-21 | 5.72e-21 | 123 |
| 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 |
| PSMA2 | SNV | Missense_Mutation | novel | c.474G>C | p.Trp158Cys | p.W158C | P25787 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1XW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD |
| PSMA2 | SNV | Missense_Mutation | novel | c.643G>A | p.Glu215Lys | p.E215K | P25787 | protein_coding | tolerated(0.36) | benign(0.001) | TCGA-OL-A5DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA2 | insertion | Frame_Shift_Ins | novel | c.278_279insTTACTTCACTTTTTGTGCCATTTCAGGAGGGAAA | p.Ala94TyrfsTer59 | p.A94Yfs*59 | P25787 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| PSMA2 | SNV | Missense_Mutation | c.383N>A | p.Arg128His | p.R128H | P25787 | protein_coding | deleterious(0.03) | benign(0.095) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| PSMA2 | SNV | Missense_Mutation | novel | c.503T>G | p.Val168Gly | p.V168G | P25787 | protein_coding | tolerated(0.38) | benign(0.09) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PSMA2 | SNV | Missense_Mutation | c.323C>A | p.Ala108Asp | p.A108D | P25787 | protein_coding | tolerated(0.53) | benign(0.129) | TCGA-F4-6570-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMA2 | SNV | Missense_Mutation | novel | c.244G>A | p.Asp82Asn | p.D82N | P25787 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PSMA2 | SNV | Missense_Mutation | novel | c.495G>T | p.Lys165Asn | p.K165N | P25787 | protein_coding | deleterious(0.04) | benign(0.308) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| PSMA2 | SNV | Missense_Mutation | novel | c.681N>T | p.Lys227Asn | p.K227N | P25787 | protein_coding | tolerated(0.18) | possibly_damaging(0.494) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PSMA2 | SNV | Missense_Mutation | c.383N>A | p.Arg128His | p.R128H | P25787 | protein_coding | deleterious(0.03) | benign(0.095) | TCGA-BG-A0LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| 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 |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL371405 | MARIZOMIB | |
| 5683 | PSMA2 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL325041 | BORTEZOMIB |
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