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Gene: PSMB4 |
Gene summary for PSMB4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMB4 | Gene ID | 5692 |
| Gene name | proteasome 20S subunit beta 4 | |
| Gene Alias | HN3 | |
| Cytomap | 1q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0002376 | UniProtAcc | A0A140VK46 |
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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 |
| 5692 | PSMB4 | GSM4909285 | Human | Breast | IDC | 3.92e-24 | 6.08e-01 | 0.21 |
| 5692 | PSMB4 | GSM4909287 | Human | Breast | IDC | 4.29e-06 | 3.98e-01 | 0.2057 |
| 5692 | PSMB4 | GSM4909296 | Human | Breast | IDC | 4.76e-07 | 2.69e-02 | 0.1524 |
| 5692 | PSMB4 | GSM4909297 | Human | Breast | IDC | 3.73e-12 | -1.58e-01 | 0.1517 |
| 5692 | PSMB4 | GSM4909301 | Human | Breast | IDC | 5.93e-03 | -2.28e-01 | 0.1577 |
| 5692 | PSMB4 | GSM4909311 | Human | Breast | IDC | 8.87e-27 | -1.43e-01 | 0.1534 |
| 5692 | PSMB4 | GSM4909312 | Human | Breast | IDC | 5.51e-11 | -6.88e-02 | 0.1552 |
| 5692 | PSMB4 | GSM4909313 | Human | Breast | IDC | 3.12e-04 | -8.58e-02 | 0.0391 |
| 5692 | PSMB4 | GSM4909318 | Human | Breast | IDC | 3.92e-03 | 1.71e-02 | 0.2031 |
| 5692 | PSMB4 | GSM4909319 | Human | Breast | IDC | 4.14e-38 | -1.61e-01 | 0.1563 |
| 5692 | PSMB4 | GSM4909320 | Human | Breast | IDC | 5.12e-06 | -1.21e-01 | 0.1575 |
| 5692 | PSMB4 | GSM4909321 | Human | Breast | IDC | 2.32e-14 | 6.35e-02 | 0.1559 |
| 5692 | PSMB4 | brca1 | Human | Breast | Precancer | 2.97e-02 | 3.45e-01 | -0.0338 |
| 5692 | PSMB4 | brca2 | Human | Breast | Precancer | 9.33e-05 | 2.59e-01 | -0.024 |
| 5692 | PSMB4 | M2 | Human | Breast | IDC | 1.58e-21 | 7.48e-01 | 0.21 |
| 5692 | PSMB4 | M5 | Human | Breast | IDC | 2.45e-05 | 6.01e-01 | 0.1598 |
| 5692 | PSMB4 | NCCBC11 | Human | Breast | DCIS | 1.34e-03 | 2.19e-01 | 0.1232 |
| 5692 | PSMB4 | NCCBC14 | Human | Breast | DCIS | 1.97e-11 | 2.56e-01 | 0.2021 |
| 5692 | PSMB4 | NCCBC2 | Human | Breast | DCIS | 3.47e-03 | -2.02e-01 | 0.1554 |
| 5692 | PSMB4 | NCCBC3 | Human | Breast | DCIS | 1.22e-02 | 4.43e-02 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:0050727 | Breast | Precancer | regulation of inflammatory response | 44/1080 | 386/18723 | 1.26e-05 | 3.22e-04 | 44 |
| GO:00026836 | Breast | Precancer | negative regulation of immune system process | 41/1080 | 434/18723 | 1.33e-03 | 1.40e-02 | 41 |
| GO:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:000268311 | Breast | IDC | negative regulation of immune system process | 55/1434 | 434/18723 | 1.53e-04 | 2.67e-03 | 55 |
| GO:00507271 | Breast | IDC | regulation of inflammatory response | 48/1434 | 386/18723 | 5.99e-04 | 7.54e-03 | 48 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:000268321 | Breast | DCIS | negative regulation of immune system process | 57/1390 | 434/18723 | 1.81e-05 | 4.35e-04 | 57 |
| GO:00507272 | Breast | DCIS | regulation of inflammatory response | 46/1390 | 386/18723 | 9.91e-04 | 1.10e-02 | 46 |
| GO:00321021 | Breast | DCIS | negative regulation of response to external stimulus | 46/1390 | 420/18723 | 5.19e-03 | 3.81e-02 | 46 |
| GO:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
| GO:00104981 | Colorectum | SER | proteasomal protein catabolic process | 132/2897 | 490/18723 | 3.08e-11 | 5.55e-09 | 132 |
| GO:00104982 | Colorectum | MSS | proteasomal protein catabolic process | 157/3467 | 490/18723 | 2.39e-13 | 5.25e-11 | 157 |
| GO:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
| GO:001049816 | Endometrium | AEH | proteasomal protein catabolic process | 108/2100 | 490/18723 | 2.73e-12 | 4.67e-10 | 108 |
| GO:00026838 | Endometrium | AEH | negative regulation of immune system process | 69/2100 | 434/18723 | 1.76e-03 | 1.41e-02 | 69 |
| GO:001049817 | Endometrium | EEC | proteasomal protein catabolic process | 112/2168 | 490/18723 | 6.99e-13 | 1.40e-10 | 112 |
| GO:000268313 | Endometrium | EEC | negative regulation of immune system process | 72/2168 | 434/18723 | 1.04e-03 | 9.13e-03 | 72 |
| 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 |
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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 |
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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 |
| PSMB4 | SNV | Missense_Mutation | c.124N>G | p.Pro42Ala | p.P42A | P28070 | protein_coding | tolerated(0.54) | benign(0.005) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| PSMB4 | insertion | In_Frame_Ins | novel | c.233_234insAAAATCAGAAGCGCAGCTCAGTGCGCGGAAAGA | p.Leu78_Ala79insLysSerGluAlaGlnLeuSerAlaArgLysGlu | p.L78_A79insKSEAQLSARKE | P28070 | protein_coding | TCGA-A8-A09X-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | ||
| PSMB4 | SNV | Missense_Mutation | rs546112706 | c.632N>A | p.Arg211His | p.R211H | P28070 | protein_coding | tolerated(0.21) | possibly_damaging(0.469) | TCGA-5M-AAT4-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
| PSMB4 | SNV | Missense_Mutation | c.434N>A | p.Arg145His | p.R145H | P28070 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMB4 | SNV | Missense_Mutation | novel | c.269N>C | p.Val90Ala | p.V90A | P28070 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-AG-A032-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Targeted Molecular therapy | bevacizumab | PD |
| PSMB4 | SNV | Missense_Mutation | rs144372831 | c.703N>A | p.Ala235Thr | p.A235T | P28070 | protein_coding | deleterious(0.04) | benign(0.356) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PSMB4 | SNV | Missense_Mutation | rs780019985 | c.634G>A | p.Asp212Asn | p.D212N | P28070 | protein_coding | tolerated(0.37) | benign(0) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMB4 | SNV | Missense_Mutation | c.334N>A | p.Leu112Ile | p.L112I | P28070 | protein_coding | tolerated(1) | benign(0.04) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMB4 | SNV | Missense_Mutation | novel | c.56N>T | p.Gly19Val | p.G19V | P28070 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| PSMB4 | SNV | Missense_Mutation | c.193G>T | p.Val65Leu | p.V65L | P28070 | protein_coding | deleterious(0.01) | possibly_damaging(0.778) | TCGA-BS-A0TC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| 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 |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL371405 | MARIZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5692 | PSMB4 | DRUGGABLE GENOME, PROTEASE | BORTEZOMIB | BORTEZOMIB | 24524217 |
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