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Gene: PSMB1 |
Gene summary for PSMB1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMB1 | Gene ID | 5689 |
| Gene name | proteasome 20S subunit beta 1 | |
| Gene Alias | HC5 | |
| Cytomap | 6q27 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | A0A140VK45 |
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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 |
| 5689 | PSMB1 | GSM4909285 | Human | Breast | IDC | 1.71e-30 | 5.99e-01 | 0.21 |
| 5689 | PSMB1 | GSM4909286 | Human | Breast | IDC | 2.40e-02 | 1.46e-01 | 0.1081 |
| 5689 | PSMB1 | GSM4909288 | Human | Breast | IDC | 2.40e-03 | 3.24e-02 | 0.0988 |
| 5689 | PSMB1 | GSM4909294 | Human | Breast | IDC | 7.56e-09 | 1.07e-01 | 0.2022 |
| 5689 | PSMB1 | GSM4909296 | Human | Breast | IDC | 2.43e-12 | -3.10e-01 | 0.1524 |
| 5689 | PSMB1 | GSM4909297 | Human | Breast | IDC | 1.10e-27 | -4.55e-01 | 0.1517 |
| 5689 | PSMB1 | GSM4909298 | Human | Breast | IDC | 3.81e-02 | -1.65e-01 | 0.1551 |
| 5689 | PSMB1 | GSM4909302 | Human | Breast | IDC | 8.99e-05 | -4.15e-01 | 0.1545 |
| 5689 | PSMB1 | GSM4909308 | Human | Breast | IDC | 2.48e-06 | 2.83e-01 | 0.158 |
| 5689 | PSMB1 | GSM4909311 | Human | Breast | IDC | 2.22e-48 | -4.76e-01 | 0.1534 |
| 5689 | PSMB1 | GSM4909312 | Human | Breast | IDC | 5.39e-15 | -2.09e-01 | 0.1552 |
| 5689 | PSMB1 | GSM4909313 | Human | Breast | IDC | 2.81e-02 | -3.39e-01 | 0.0391 |
| 5689 | PSMB1 | GSM4909315 | Human | Breast | IDC | 2.21e-18 | 4.90e-01 | 0.21 |
| 5689 | PSMB1 | GSM4909316 | Human | Breast | IDC | 2.29e-08 | 2.52e-01 | 0.21 |
| 5689 | PSMB1 | GSM4909318 | Human | Breast | IDC | 2.25e-05 | 3.74e-01 | 0.2031 |
| 5689 | PSMB1 | GSM4909319 | Human | Breast | IDC | 9.13e-57 | -6.21e-01 | 0.1563 |
| 5689 | PSMB1 | GSM4909320 | Human | Breast | IDC | 1.08e-09 | -4.82e-01 | 0.1575 |
| 5689 | PSMB1 | GSM4909321 | Human | Breast | IDC | 7.52e-17 | -5.21e-02 | 0.1559 |
| 5689 | PSMB1 | brca1 | Human | Breast | Precancer | 1.87e-55 | 7.72e-01 | -0.0338 |
| 5689 | PSMB1 | brca2 | Human | Breast | Precancer | 5.61e-23 | 5.15e-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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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: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:00421108 | Cervix | CC | T cell activation | 107/2311 | 487/18723 | 1.24e-09 | 1.46e-07 | 107 |
| GO:00420988 | Cervix | CC | T cell proliferation | 49/2311 | 199/18723 | 1.32e-06 | 4.49e-05 | 49 |
| GO:00706617 | Cervix | CC | leukocyte proliferation | 65/2311 | 318/18723 | 2.56e-05 | 4.32e-04 | 65 |
| GO:00466516 | Cervix | CC | lymphocyte proliferation | 59/2311 | 288/18723 | 5.53e-05 | 8.10e-04 | 59 |
| GO:00329435 | Cervix | CC | mononuclear cell proliferation | 59/2311 | 291/18723 | 7.51e-05 | 1.03e-03 | 59 |
| GO:00069597 | Cervix | CC | humoral immune response | 54/2311 | 317/18723 | 8.57e-03 | 4.42e-02 | 54 |
| 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: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:004211018 | Esophagus | ESCC | T cell activation | 256/8552 | 487/18723 | 1.18e-03 | 5.87e-03 | 256 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
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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 |
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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 |
| PSMB1 | insertion | Nonsense_Mutation | novel | c.236_237insGGAGTATATAGTATATTTATTTAACTGACAC | p.Ile80GlufsTer9 | p.I80Efs*9 | P20618 | protein_coding | TCGA-A2-A0EY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| PSMB1 | SNV | Missense_Mutation | c.568G>C | p.Glu190Gln | p.E190Q | P20618 | protein_coding | tolerated(0.28) | benign(0.011) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PSMB1 | SNV | Missense_Mutation | rs775486561 | c.665G>A | p.Arg222Gln | p.R222Q | P20618 | protein_coding | tolerated(0.61) | benign(0.113) | TCGA-A6-2679-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PSMB1 | SNV | Missense_Mutation | c.142N>G | p.Phe48Val | p.F48V | P20618 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-6141-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fu | SD | |
| PSMB1 | SNV | Missense_Mutation | c.545N>A | p.Gly182Asp | p.G182D | P20618 | protein_coding | deleterious(0.01) | probably_damaging(0.965) | TCGA-DM-A28M-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PSMB1 | SNV | Missense_Mutation | novel | c.316N>G | p.Ser106Ala | p.S106A | P20618 | protein_coding | tolerated(0.33) | possibly_damaging(0.877) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PSMB1 | SNV | Missense_Mutation | novel | c.552G>T | p.Lys184Asn | p.K184N | P20618 | protein_coding | deleterious(0) | possibly_damaging(0.817) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| PSMB1 | SNV | Missense_Mutation | c.320N>C | p.Asn107Thr | p.N107T | P20618 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-B5-A0JY-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| PSMB1 | SNV | Missense_Mutation | novel | c.554A>G | p.Asn185Ser | p.N185S | P20618 | protein_coding | deleterious(0) | benign(0.338) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMB1 | SNV | Missense_Mutation | novel | c.415N>A | p.Gly139Ser | p.G139S | P20618 | protein_coding | deleterious(0.02) | possibly_damaging(0.695) | TCGA-D1-A17Q-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 |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | MLN-9708 | IXAZOMIB CITRATE | ||
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL371405 | MARIZOMIB | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | BORTEZOMIB | BORTEZOMIB | ||
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | MG-132 | MG-132 | 24321833,18801655 | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5689 | PSMB1 | PROTEASE, DRUGGABLE GENOME, ENZYME | CARFILZOMIB | CARFILZOMIB |
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