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Gene: PSMC5 |
Gene summary for PSMC5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMC5 | Gene ID | 5705 |
| Gene name | proteasome 26S subunit, ATPase 5 | |
| Gene Alias | RPT6 | |
| Cytomap | 17q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | P62195 |
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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 |
| 5705 | PSMC5 | GSM4909286 | Human | Breast | IDC | 3.56e-03 | 4.40e-02 | 0.1081 |
| 5705 | PSMC5 | GSM4909296 | Human | Breast | IDC | 4.90e-08 | -2.38e-01 | 0.1524 |
| 5705 | PSMC5 | GSM4909297 | Human | Breast | IDC | 1.81e-09 | -6.68e-02 | 0.1517 |
| 5705 | PSMC5 | GSM4909301 | Human | Breast | IDC | 4.83e-06 | -2.31e-01 | 0.1577 |
| 5705 | PSMC5 | GSM4909308 | Human | Breast | IDC | 1.16e-03 | 2.90e-01 | 0.158 |
| 5705 | PSMC5 | GSM4909311 | Human | Breast | IDC | 8.99e-19 | -2.01e-01 | 0.1534 |
| 5705 | PSMC5 | GSM4909312 | Human | Breast | IDC | 4.44e-06 | -8.16e-02 | 0.1552 |
| 5705 | PSMC5 | GSM4909317 | Human | Breast | IDC | 2.86e-02 | 2.68e-01 | 0.1355 |
| 5705 | PSMC5 | GSM4909318 | Human | Breast | IDC | 1.69e-03 | 2.77e-01 | 0.2031 |
| 5705 | PSMC5 | GSM4909319 | Human | Breast | IDC | 4.24e-35 | -9.46e-02 | 0.1563 |
| 5705 | PSMC5 | GSM4909320 | Human | Breast | IDC | 1.81e-05 | 1.45e-01 | 0.1575 |
| 5705 | PSMC5 | GSM4909321 | Human | Breast | IDC | 9.35e-13 | 2.09e-01 | 0.1559 |
| 5705 | PSMC5 | brca1 | Human | Breast | Precancer | 1.15e-17 | 5.44e-01 | -0.0338 |
| 5705 | PSMC5 | brca2 | Human | Breast | Precancer | 1.30e-14 | 4.28e-01 | -0.024 |
| 5705 | PSMC5 | brca3 | Human | Breast | Precancer | 7.82e-07 | 3.17e-01 | -0.0263 |
| 5705 | PSMC5 | M1 | Human | Breast | IDC | 3.46e-06 | 4.13e-01 | 0.1577 |
| 5705 | PSMC5 | M2 | Human | Breast | IDC | 1.24e-07 | 5.10e-01 | 0.21 |
| 5705 | PSMC5 | NCCBC14 | Human | Breast | DCIS | 1.14e-08 | 1.60e-01 | 0.2021 |
| 5705 | PSMC5 | NCCBC2 | Human | Breast | DCIS | 3.43e-04 | 1.93e-01 | 0.1554 |
| 5705 | PSMC5 | NCCBC5 | Human | Breast | DCIS | 2.02e-08 | 1.40e-02 | 0.2046 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 | ||
| 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:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
| GO:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:19033629 | Breast | Precancer | regulation of cellular protein catabolic process | 36/1080 | 255/18723 | 6.03e-07 | 2.55e-05 | 36 |
| GO:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
| GO:19030509 | Breast | Precancer | regulation of proteolysis involved in cellular protein catabolic process | 31/1080 | 221/18723 | 4.10e-06 | 1.27e-04 | 31 |
| GO:00611369 | Breast | Precancer | regulation of proteasomal protein catabolic process | 24/1080 | 187/18723 | 1.99e-04 | 3.14e-03 | 24 |
| GO:00431619 | Breast | Precancer | proteasome-mediated ubiquitin-dependent protein catabolic process | 42/1080 | 412/18723 | 2.49e-04 | 3.72e-03 | 42 |
| GO:00098969 | Breast | Precancer | positive regulation of catabolic process | 48/1080 | 492/18723 | 2.62e-04 | 3.84e-03 | 48 |
| GO:00313319 | Breast | Precancer | positive regulation of cellular catabolic process | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
| GO:19033649 | Breast | Precancer | positive regulation of cellular protein catabolic process | 20/1080 | 155/18723 | 6.10e-04 | 7.67e-03 | 20 |
| GO:19030527 | Breast | Precancer | positive regulation of proteolysis involved in cellular protein catabolic process | 17/1080 | 133/18723 | 1.68e-03 | 1.70e-02 | 17 |
| GO:00457329 | Breast | Precancer | positive regulation of protein catabolic process | 25/1080 | 231/18723 | 1.87e-03 | 1.82e-02 | 25 |
| GO:00708417 | Breast | Precancer | inclusion body assembly | 6/1080 | 24/18723 | 1.99e-03 | 1.90e-02 | 6 |
| GO:00900836 | Breast | Precancer | regulation of inclusion body assembly | 5/1080 | 17/18723 | 2.19e-03 | 2.06e-02 | 5 |
| GO:19018007 | Breast | Precancer | positive regulation of proteasomal protein catabolic process | 15/1080 | 114/18723 | 2.31e-03 | 2.15e-02 | 15 |
| GO:004586214 | Breast | IDC | positive regulation of proteolysis | 66/1434 | 372/18723 | 9.76e-11 | 1.29e-08 | 66 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:004217614 | Breast | IDC | regulation of protein catabolic process | 63/1434 | 391/18723 | 1.32e-08 | 9.61e-07 | 63 |
| GO:190336214 | Breast | IDC | regulation of cellular protein catabolic process | 46/1434 | 255/18723 | 4.00e-08 | 2.68e-06 | 46 |
| GO:190305014 | Breast | IDC | regulation of proteolysis involved in cellular protein catabolic process | 41/1434 | 221/18723 | 9.77e-08 | 5.84e-06 | 41 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 |
| hsa0516918 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
| 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 |
| hsa0516919 | Breast | Precancer | Epstein-Barr virus infection | 35/684 | 202/8465 | 1.15e-05 | 1.26e-04 | 9.64e-05 | 35 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
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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 |
| PSMC5 | SNV | Missense_Mutation | novel | c.1206N>C | p.Lys402Asn | p.K402N | P62195 | protein_coding | tolerated(0.12) | benign(0.003) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| PSMC5 | SNV | Missense_Mutation | c.554N>C | p.Gly185Ala | p.G185A | P62195 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PSMC5 | SNV | Missense_Mutation | novel | c.397N>T | p.Pro133Ser | p.P133S | P62195 | protein_coding | tolerated(0.09) | possibly_damaging(0.601) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PSMC5 | SNV | Missense_Mutation | c.1168N>C | p.Val390Leu | p.V390L | P62195 | protein_coding | tolerated(0.06) | benign(0.081) | TCGA-E2-A14V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| PSMC5 | insertion | Nonsense_Mutation | novel | c.128_129insCAAACTGCTTCACTAGTAGGATTTCTCC | p.Arg44LysfsTer5 | p.R44Kfs*5 | P62195 | protein_coding | TCGA-A2-A0EO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PSMC5 | insertion | Frame_Shift_Ins | novel | c.512_513insCCTAACAATCTTTCCACCAGGTGTTGTTGCCT | p.Pro172LeufsTer64 | p.P172Lfs*64 | P62195 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| PSMC5 | insertion | Frame_Shift_Ins | novel | c.74_75insTATTTTA | p.Ser26IlefsTer6 | p.S26Ifs*6 | P62195 | protein_coding | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PSMC5 | insertion | Frame_Shift_Ins | novel | c.78_79insTGGGAAAATGGAGGGTTCC | p.Lys27TrpfsTer9 | p.K27Wfs*9 | P62195 | protein_coding | TCGA-A8-A0A1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| PSMC5 | SNV | Missense_Mutation | c.414G>A | p.Met138Ile | p.M138I | P62195 | protein_coding | deleterious(0.02) | benign(0.176) | TCGA-VS-A9U5-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PSMC5 | SNV | Missense_Mutation | c.526G>A | p.Glu176Lys | p.E176K | P62195 | protein_coding | tolerated(0.19) | benign(0.061) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | IXAZOMIB | IXAZOMIB | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5705 | PSMC5 | TRANSCRIPTION FACTOR BINDING, PROTEASE | inhibitor | CHEMBL451887 | CARFILZOMIB |
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