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Gene: PSMD2 |
Gene summary for PSMD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMD2 | Gene ID | 5708 |
| Gene name | proteasome 26S subunit ubiquitin receptor, non-ATPase 2 | |
| Gene Alias | P97 | |
| Cytomap | 3q27.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q13200 |
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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 |
| 5708 | PSMD2 | GSM4909281 | Human | Breast | IDC | 9.50e-21 | 6.06e-01 | 0.21 |
| 5708 | PSMD2 | GSM4909282 | Human | Breast | IDC | 1.24e-09 | 4.07e-01 | -0.0288 |
| 5708 | PSMD2 | GSM4909285 | Human | Breast | IDC | 5.24e-33 | 6.73e-01 | 0.21 |
| 5708 | PSMD2 | GSM4909287 | Human | Breast | IDC | 2.77e-06 | 3.25e-01 | 0.2057 |
| 5708 | PSMD2 | GSM4909288 | Human | Breast | IDC | 5.57e-07 | 3.64e-01 | 0.0988 |
| 5708 | PSMD2 | GSM4909293 | Human | Breast | IDC | 1.34e-13 | 3.83e-01 | 0.1581 |
| 5708 | PSMD2 | GSM4909304 | Human | Breast | IDC | 4.82e-10 | 3.62e-01 | 0.1636 |
| 5708 | PSMD2 | GSM4909311 | Human | Breast | IDC | 2.45e-11 | -1.37e-01 | 0.1534 |
| 5708 | PSMD2 | GSM4909312 | Human | Breast | IDC | 4.11e-04 | -4.40e-03 | 0.1552 |
| 5708 | PSMD2 | GSM4909317 | Human | Breast | IDC | 2.80e-07 | 3.22e-01 | 0.1355 |
| 5708 | PSMD2 | GSM4909319 | Human | Breast | IDC | 5.22e-17 | -1.68e-01 | 0.1563 |
| 5708 | PSMD2 | GSM4909321 | Human | Breast | IDC | 2.43e-04 | 5.31e-03 | 0.1559 |
| 5708 | PSMD2 | brca1 | Human | Breast | Precancer | 7.41e-11 | 4.76e-01 | -0.0338 |
| 5708 | PSMD2 | brca2 | Human | Breast | Precancer | 6.96e-13 | 4.45e-01 | -0.024 |
| 5708 | PSMD2 | brca3 | Human | Breast | Precancer | 3.42e-11 | 3.85e-01 | -0.0263 |
| 5708 | PSMD2 | M2 | Human | Breast | IDC | 2.28e-14 | 7.05e-01 | 0.21 |
| 5708 | PSMD2 | NCCBC14 | Human | Breast | DCIS | 1.17e-06 | 2.67e-01 | 0.2021 |
| 5708 | PSMD2 | NCCBC2 | Human | Breast | DCIS | 3.96e-06 | 1.02e-01 | 0.1554 |
| 5708 | PSMD2 | NCCBC5 | Human | Breast | DCIS | 2.98e-05 | 7.28e-02 | 0.2046 |
| 5708 | PSMD2 | NCCBC6 | Human | Breast | DCIS | 5.62e-07 | 4.59e-01 | 0.2095 |
| 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:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
| GO:00431619 | Breast | Precancer | proteasome-mediated ubiquitin-dependent protein catabolic process | 42/1080 | 412/18723 | 2.49e-04 | 3.72e-03 | 42 |
| 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:004316114 | Breast | IDC | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1434 | 412/18723 | 9.55e-06 | 2.68e-04 | 57 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:004217624 | Breast | DCIS | regulation of protein catabolic process | 62/1390 | 391/18723 | 9.98e-09 | 7.53e-07 | 62 |
| GO:004316124 | Breast | DCIS | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1390 | 412/18723 | 3.76e-06 | 1.16e-04 | 57 |
| GO:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
| 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:00421761 | Colorectum | SER | regulation of protein catabolic process | 126/2897 | 391/18723 | 5.33e-17 | 2.52e-14 | 126 |
| GO:00104981 | Colorectum | SER | proteasomal protein catabolic process | 132/2897 | 490/18723 | 3.08e-11 | 5.55e-09 | 132 |
| GO:00431611 | Colorectum | SER | proteasome-mediated ubiquitin-dependent protein catabolic process | 105/2897 | 412/18723 | 7.48e-08 | 4.70e-06 | 105 |
| GO:00421762 | Colorectum | MSS | regulation of protein catabolic process | 145/3467 | 391/18723 | 2.03e-18 | 1.17e-15 | 145 |
| 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:00421763 | Colorectum | MSI-H | regulation of protein catabolic process | 65/1319 | 391/18723 | 6.96e-11 | 1.29e-08 | 65 |
| GO:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
| Page: 1 2 3 |
| 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 |
| PSMD2 | SNV | Missense_Mutation | c.458N>T | p.Ser153Leu | p.S153L | Q13200 | protein_coding | tolerated(0.08) | possibly_damaging(0.879) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PSMD2 | SNV | Missense_Mutation | c.301N>G | p.Pro101Ala | p.P101A | Q13200 | protein_coding | deleterious(0.01) | probably_damaging(0.971) | TCGA-E9-A1R2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxotere | CR | |
| PSMD2 | insertion | In_Frame_Ins | novel | c.908_909insCAT | p.Val303_Phe304insMet | p.V303_F304insM | Q13200 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| PSMD2 | insertion | Frame_Shift_Ins | novel | c.909_910insAGTATGTCAGGTAAGATCT | p.Phe304SerfsTer12 | p.F304Sfs*12 | Q13200 | protein_coding | TCGA-A7-A0CE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | ||
| PSMD2 | insertion | Nonsense_Mutation | novel | c.1343_1344insATGAGTGCCTGGGACTT | p.Cys448Ter | p.C448* | Q13200 | protein_coding | TCGA-BH-A0E2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | ||
| PSMD2 | SNV | Missense_Mutation | novel | c.1209G>T | p.Lys403Asn | p.K403N | Q13200 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMD2 | SNV | Missense_Mutation | novel | c.2534G>A | p.Arg845His | p.R845H | Q13200 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMD2 | SNV | Missense_Mutation | novel | c.2555T>C | p.Val852Ala | p.V852A | Q13200 | protein_coding | deleterious(0) | possibly_damaging(0.9) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMD2 | SNV | Missense_Mutation | novel | c.1908N>A | p.Asp636Glu | p.D636E | Q13200 | protein_coding | tolerated(0.53) | benign(0.001) | TCGA-C5-A2LT-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PSMD2 | SNV | Missense_Mutation | novel | c.412G>A | p.Glu138Lys | p.E138K | Q13200 | protein_coding | deleterious(0.02) | benign(0) | TCGA-C5-A8XJ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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 |
| 5708 | PSMD2 | NA | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5708 | PSMD2 | NA | MLN-9708 | IXAZOMIB CITRATE | ||
| 5708 | PSMD2 | NA | BORTEZOMIB | BORTEZOMIB | ||
| 5708 | PSMD2 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5708 | PSMD2 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5708 | PSMD2 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5708 | PSMD2 | NA | BORTEZOMIB | BORTEZOMIB | ||
| 5708 | PSMD2 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5708 | PSMD2 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5708 | PSMD2 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB |
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