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Gene: PSMB5 |
Gene summary for PSMB5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMB5 | Gene ID | 5693 |
| Gene name | proteasome 20S subunit beta 5 | |
| Gene Alias | LMPX | |
| Cytomap | 14q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | A0A140VJS7 |
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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 |
| 5693 | PSMB5 | GSM4909282 | Human | Breast | IDC | 1.10e-08 | 4.38e-01 | -0.0288 |
| 5693 | PSMB5 | GSM4909285 | Human | Breast | IDC | 2.95e-16 | 5.21e-01 | 0.21 |
| 5693 | PSMB5 | GSM4909286 | Human | Breast | IDC | 4.24e-05 | 1.40e-01 | 0.1081 |
| 5693 | PSMB5 | GSM4909288 | Human | Breast | IDC | 8.02e-06 | 1.73e-01 | 0.0988 |
| 5693 | PSMB5 | GSM4909290 | Human | Breast | IDC | 2.52e-03 | 2.84e-01 | 0.2096 |
| 5693 | PSMB5 | GSM4909291 | Human | Breast | IDC | 6.00e-122 | 1.38e+00 | 0.1753 |
| 5693 | PSMB5 | GSM4909293 | Human | Breast | IDC | 3.76e-06 | 3.54e-01 | 0.1581 |
| 5693 | PSMB5 | GSM4909294 | Human | Breast | IDC | 1.55e-02 | 1.45e-01 | 0.2022 |
| 5693 | PSMB5 | GSM4909296 | Human | Breast | IDC | 1.13e-08 | 1.66e-01 | 0.1524 |
| 5693 | PSMB5 | GSM4909297 | Human | Breast | IDC | 3.05e-12 | -1.22e-01 | 0.1517 |
| 5693 | PSMB5 | GSM4909298 | Human | Breast | IDC | 1.27e-05 | -2.86e-01 | 0.1551 |
| 5693 | PSMB5 | GSM4909308 | Human | Breast | IDC | 1.67e-02 | 2.03e-01 | 0.158 |
| 5693 | PSMB5 | GSM4909311 | Human | Breast | IDC | 2.03e-36 | -3.00e-01 | 0.1534 |
| 5693 | PSMB5 | GSM4909312 | Human | Breast | IDC | 5.62e-10 | -6.57e-02 | 0.1552 |
| 5693 | PSMB5 | GSM4909316 | Human | Breast | IDC | 6.70e-05 | 2.13e-01 | 0.21 |
| 5693 | PSMB5 | GSM4909319 | Human | Breast | IDC | 2.32e-46 | -2.39e-01 | 0.1563 |
| 5693 | PSMB5 | GSM4909320 | Human | Breast | IDC | 6.91e-10 | 1.35e-01 | 0.1575 |
| 5693 | PSMB5 | GSM4909321 | Human | Breast | IDC | 9.18e-14 | 9.40e-02 | 0.1559 |
| 5693 | PSMB5 | brca1 | Human | Breast | Precancer | 3.47e-35 | 7.25e-01 | -0.0338 |
| 5693 | PSMB5 | brca2 | Human | Breast | Precancer | 8.83e-11 | 4.22e-01 | -0.024 |
| 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 | ||
| 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:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
| GO:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:00431619 | Breast | Precancer | proteasome-mediated ubiquitin-dependent protein catabolic process | 42/1080 | 412/18723 | 2.49e-04 | 3.72e-03 | 42 |
| GO:000697914 | Breast | IDC | response to oxidative stress | 83/1434 | 446/18723 | 2.36e-14 | 7.06e-12 | 83 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:004316114 | Breast | IDC | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1434 | 412/18723 | 9.55e-06 | 2.68e-04 | 57 |
| GO:000697924 | Breast | DCIS | response to oxidative stress | 82/1390 | 446/18723 | 1.22e-14 | 3.85e-12 | 82 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:004316124 | Breast | DCIS | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1390 | 412/18723 | 3.76e-06 | 1.16e-04 | 57 |
| GO:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
| GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
| GO:0006979 | Colorectum | AD | response to oxidative stress | 145/3918 | 446/18723 | 5.16e-09 | 3.23e-07 | 145 |
| GO:00104981 | Colorectum | SER | proteasomal protein catabolic process | 132/2897 | 490/18723 | 3.08e-11 | 5.55e-09 | 132 |
| GO:00069791 | Colorectum | SER | response to oxidative stress | 114/2897 | 446/18723 | 1.75e-08 | 1.28e-06 | 114 |
| GO:00431611 | Colorectum | SER | proteasome-mediated ubiquitin-dependent protein catabolic process | 105/2897 | 412/18723 | 7.48e-08 | 4.70e-06 | 105 |
| GO:00104982 | Colorectum | MSS | proteasomal protein catabolic process | 157/3467 | 490/18723 | 2.39e-13 | 5.25e-11 | 157 |
| GO:00431612 | Colorectum | MSS | proteasome-mediated ubiquitin-dependent protein catabolic process | 127/3467 | 412/18723 | 7.70e-10 | 6.32e-08 | 127 |
| GO:00069792 | Colorectum | MSS | response to oxidative stress | 128/3467 | 446/18723 | 7.65e-08 | 3.81e-06 | 128 |
| GO:00069793 | Colorectum | MSI-H | response to oxidative stress | 68/1319 | 446/18723 | 1.17e-09 | 1.59e-07 | 68 |
| GO:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
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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 13 14 15 16 |
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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 |
| PSMB5 | SNV | Missense_Mutation | novel | c.479N>G | p.Ile160Ser | p.I160S | P28074 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PSMB5 | SNV | Missense_Mutation | c.79N>A | p.Leu27Met | p.L27M | P28074 | protein_coding | tolerated(0.16) | benign(0.193) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMB5 | SNV | Missense_Mutation | novel | c.128N>T | p.Ala43Val | p.A43V | P28074 | protein_coding | tolerated(0.45) | probably_damaging(0.97) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| PSMB5 | insertion | Nonsense_Mutation | novel | c.310_311insCATGTGGCAGTAGTGCTATTTCAAGTGTTCATTGACCATGTG | p.Met104delinsThrCysGlySerSerAlaIleSerSerValHisTerProCysVal | p.M104delinsTCGSSAISSVH*PCV | P28074 | protein_coding | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PSMB5 | deletion | Frame_Shift_Del | c.116_125delTGAGCCTGGC | p.Leu39ProfsTer31 | p.L39Pfs*31 | P28074 | protein_coding | TCGA-BH-A204-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| PSMB5 | SNV | Missense_Mutation | c.358N>T | p.Arg120Trp | p.R120W | P28074 | protein_coding | deleterious(0.01) | probably_damaging(0.949) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |
| PSMB5 | SNV | Missense_Mutation | c.630N>T | p.Gln210His | p.Q210H | P28074 | protein_coding | deleterious(0) | benign(0.219) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| PSMB5 | deletion | Frame_Shift_Del | c.320delN | p.Gly107AlafsTer29 | p.G107Afs*29 | P28074 | protein_coding | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| PSMB5 | SNV | Missense_Mutation | novel | c.493N>G | p.Lys165Glu | p.K165E | P28074 | protein_coding | tolerated(0.16) | benign(0.038) | TCGA-A5-A2K3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
| PSMB5 | SNV | Missense_Mutation | c.529G>T | p.Gly177Trp | p.G177W | P28074 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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 |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | BORTEZOMIB | BORTEZOMIB | ||
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | inhibitor | 178103992 | CARFILZOMIB | |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | inhibitor | 385612170 | KZR-616 | |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | BORTEZOMIB | BORTEZOMIB | ||
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | BELACTOSIN A | BELACTOSIN A | 23547757 | |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | CARFILZOMIB | CARFILZOMIB | ||
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | MARIZOMIB | MARIZOMIB | 24269479 | |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | OPROZOMIB | OPROZOMIB | ||
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | CLASTO-LACTACYSTIN BETA-LACTONE | CHEMBL490829 | 18801655 | |
| 5693 | PSMB5 | PROTEASE, ENZYME, DRUGGABLE GENOME | BORTEZOMIB | BORTEZOMIB | 24524217,23547757 |
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