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Gene: PSMD3 |
Gene summary for PSMD3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMD3 | Gene ID | 5709 |
| Gene name | proteasome 26S subunit, non-ATPase 3 | |
| Gene Alias | P58 | |
| Cytomap | 17q21.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | O43242 |
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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 |
| 5709 | PSMD3 | GSM4909291 | Human | Breast | IDC | 5.30e-66 | 1.28e+00 | 0.1753 |
| 5709 | PSMD3 | GSM4909292 | Human | Breast | IDC | 2.23e-08 | 8.07e-01 | 0.1236 |
| 5709 | PSMD3 | GSM4909294 | Human | Breast | IDC | 2.07e-23 | 6.32e-01 | 0.2022 |
| 5709 | PSMD3 | GSM4909296 | Human | Breast | IDC | 1.99e-10 | -2.17e-01 | 0.1524 |
| 5709 | PSMD3 | GSM4909297 | Human | Breast | IDC | 2.01e-04 | -6.31e-02 | 0.1517 |
| 5709 | PSMD3 | GSM4909311 | Human | Breast | IDC | 7.08e-13 | -1.40e-01 | 0.1534 |
| 5709 | PSMD3 | GSM4909312 | Human | Breast | IDC | 2.96e-04 | -6.78e-02 | 0.1552 |
| 5709 | PSMD3 | GSM4909319 | Human | Breast | IDC | 1.73e-20 | -1.03e-01 | 0.1563 |
| 5709 | PSMD3 | GSM4909320 | Human | Breast | IDC | 3.30e-04 | -1.78e-01 | 0.1575 |
| 5709 | PSMD3 | GSM4909321 | Human | Breast | IDC | 8.66e-07 | 4.95e-02 | 0.1559 |
| 5709 | PSMD3 | brca1 | Human | Breast | Precancer | 7.99e-05 | 3.77e-01 | -0.0338 |
| 5709 | PSMD3 | brca2 | Human | Breast | Precancer | 7.97e-09 | 3.91e-01 | -0.024 |
| 5709 | PSMD3 | brca3 | Human | Breast | Precancer | 1.72e-04 | 3.26e-01 | -0.0263 |
| 5709 | PSMD3 | NCCBC14 | Human | Breast | DCIS | 7.06e-74 | 1.34e+00 | 0.2021 |
| 5709 | PSMD3 | NCCBC5 | Human | Breast | DCIS | 5.77e-21 | 5.61e-01 | 0.2046 |
| 5709 | PSMD3 | P1 | Human | Breast | IDC | 4.09e-05 | -1.62e-01 | 0.1527 |
| 5709 | PSMD3 | DCIS2 | Human | Breast | DCIS | 5.32e-33 | 1.38e-01 | 0.0085 |
| 5709 | PSMD3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.25e-03 | 2.74e-01 | -0.1808 |
| 5709 | PSMD3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.77e-03 | 3.61e-01 | -0.0811 |
| 5709 | PSMD3 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.44e-17 | 4.39e-01 | -0.1954 |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 | ||
| 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 | ||
| 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:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
| GO:004217614 | Breast | IDC | regulation of protein catabolic process | 63/1434 | 391/18723 | 1.32e-08 | 9.61e-07 | 63 |
| GO:004217624 | Breast | DCIS | regulation of protein catabolic process | 62/1390 | 391/18723 | 9.98e-09 | 7.53e-07 | 62 |
| GO:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
| GO:00421761 | Colorectum | SER | regulation of protein catabolic process | 126/2897 | 391/18723 | 5.33e-17 | 2.52e-14 | 126 |
| GO:00421762 | Colorectum | MSS | regulation of protein catabolic process | 145/3467 | 391/18723 | 2.03e-18 | 1.17e-15 | 145 |
| GO:004217627 | Esophagus | HGIN | regulation of protein catabolic process | 119/2587 | 391/18723 | 8.09e-18 | 2.43e-15 | 119 |
| GO:0042176111 | Esophagus | ESCC | regulation of protein catabolic process | 280/8552 | 391/18723 | 8.65e-26 | 2.39e-23 | 280 |
| GO:004217612 | Liver | Cirrhotic | regulation of protein catabolic process | 181/4634 | 391/18723 | 7.94e-21 | 2.77e-18 | 181 |
| GO:004217622 | Liver | HCC | regulation of protein catabolic process | 267/7958 | 391/18723 | 2.45e-25 | 7.38e-23 | 267 |
| GO:004217620 | Oral cavity | OSCC | regulation of protein catabolic process | 254/7305 | 391/18723 | 1.07e-25 | 3.22e-23 | 254 |
| GO:0042176110 | Oral cavity | LP | regulation of protein catabolic process | 177/4623 | 391/18723 | 3.00e-19 | 5.87e-17 | 177 |
| GO:004217629 | Skin | cSCC | regulation of protein catabolic process | 198/4864 | 391/18723 | 6.03e-26 | 1.89e-23 | 198 |
| GO:0042176113 | Thyroid | PTC | regulation of protein catabolic process | 231/5968 | 391/18723 | 4.76e-29 | 2.14e-26 | 231 |
| GO:004217635 | Thyroid | ATC | regulation of protein catabolic process | 239/6293 | 391/18723 | 2.63e-29 | 1.85e-26 | 239 |
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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 |
| 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 |
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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 |
| PSMD3 | SNV | Missense_Mutation | c.601C>G | p.Arg201Gly | p.R201G | O43242 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-AR-A1AT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | anastrozole | SD | |
| PSMD3 | SNV | Missense_Mutation | novel | c.865N>T | p.Leu289Phe | p.L289F | O43242 | protein_coding | tolerated(0.05) | benign(0.014) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| PSMD3 | SNV | Missense_Mutation | rs143390511 | c.923N>T | p.Thr308Met | p.T308M | O43242 | protein_coding | deleterious(0.01) | benign(0.074) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMD3 | SNV | Missense_Mutation | novel | c.579N>C | p.Gln193His | p.Q193H | O43242 | protein_coding | deleterious(0) | benign(0.067) | TCGA-4J-AA1J-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMD3 | SNV | Missense_Mutation | c.1222C>T | p.Arg408Cys | p.R408C | O43242 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD3 | SNV | Missense_Mutation | c.690C>A | p.Phe230Leu | p.F230L | O43242 | protein_coding | tolerated(0.62) | benign(0) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| PSMD3 | SNV | Missense_Mutation | c.940C>T | p.Arg314Cys | p.R314C | O43242 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DM-A1D0-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD3 | SNV | Missense_Mutation | rs762214384 | c.449N>A | p.Arg150His | p.R150H | O43242 | protein_coding | deleterious(0.04) | possibly_damaging(0.648) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| PSMD3 | SNV | Missense_Mutation | rs749507799 | c.499N>A | p.Leu167Ile | p.L167I | O43242 | protein_coding | tolerated(0.21) | benign(0.085) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PSMD3 | SNV | Missense_Mutation | novel | c.1436N>A | p.Arg479His | p.R479H | O43242 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | 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 |
| 5709 | PSMD3 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5709 | PSMD3 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5709 | PSMD3 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5709 | PSMD3 | NA | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5709 | PSMD3 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5709 | PSMD3 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5709 | PSMD3 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5709 | PSMD3 | NA | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE |
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