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Gene: PSMD6 |
Gene summary for PSMD6 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMD6 | Gene ID | 9861 |
| Gene name | proteasome 26S subunit, non-ATPase 6 | |
| Gene Alias | Rpn7 | |
| Cytomap | 3p14.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q15008 |
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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 |
| 9861 | PSMD6 | LZE4T | Human | Esophagus | ESCC | 6.33e-18 | 4.59e-01 | 0.0811 |
| 9861 | PSMD6 | LZE5T | Human | Esophagus | ESCC | 1.00e-03 | 1.79e-01 | 0.0514 |
| 9861 | PSMD6 | LZE7T | Human | Esophagus | ESCC | 1.42e-04 | 4.76e-01 | 0.0667 |
| 9861 | PSMD6 | LZE8T | Human | Esophagus | ESCC | 1.98e-11 | 2.44e-01 | 0.067 |
| 9861 | PSMD6 | LZE20T | Human | Esophagus | ESCC | 3.29e-07 | 8.62e-02 | 0.0662 |
| 9861 | PSMD6 | LZE22D1 | Human | Esophagus | HGIN | 4.54e-02 | 1.92e-03 | 0.0595 |
| 9861 | PSMD6 | LZE24T | Human | Esophagus | ESCC | 1.15e-20 | 6.79e-01 | 0.0596 |
| 9861 | PSMD6 | LZE21T | Human | Esophagus | ESCC | 1.01e-03 | 1.93e-01 | 0.0655 |
| 9861 | PSMD6 | LZE6T | Human | Esophagus | ESCC | 4.00e-07 | 3.79e-01 | 0.0845 |
| 9861 | PSMD6 | P1T-E | Human | Esophagus | ESCC | 3.63e-08 | 4.48e-01 | 0.0875 |
| 9861 | PSMD6 | P2T-E | Human | Esophagus | ESCC | 7.25e-37 | 7.79e-01 | 0.1177 |
| 9861 | PSMD6 | P4T-E | Human | Esophagus | ESCC | 3.70e-44 | 1.10e+00 | 0.1323 |
| 9861 | PSMD6 | P5T-E | Human | Esophagus | ESCC | 3.79e-26 | 6.05e-01 | 0.1327 |
| 9861 | PSMD6 | P8T-E | Human | Esophagus | ESCC | 1.48e-25 | 3.61e-01 | 0.0889 |
| 9861 | PSMD6 | P9T-E | Human | Esophagus | ESCC | 8.35e-26 | 5.47e-01 | 0.1131 |
| 9861 | PSMD6 | P10T-E | Human | Esophagus | ESCC | 5.75e-26 | 5.15e-01 | 0.116 |
| 9861 | PSMD6 | P11T-E | Human | Esophagus | ESCC | 1.87e-14 | 7.90e-01 | 0.1426 |
| 9861 | PSMD6 | P12T-E | Human | Esophagus | ESCC | 1.17e-40 | 8.87e-01 | 0.1122 |
| 9861 | PSMD6 | P15T-E | Human | Esophagus | ESCC | 2.08e-31 | 5.32e-01 | 0.1149 |
| 9861 | PSMD6 | P16T-E | Human | Esophagus | ESCC | 1.16e-32 | 5.60e-01 | 0.1153 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
| GO:004316126 | Esophagus | HGIN | proteasome-mediated ubiquitin-dependent protein catabolic process | 114/2587 | 412/18723 | 7.00e-14 | 1.20e-11 | 114 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:0043161111 | Esophagus | ESCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 312/8552 | 412/18723 | 3.53e-36 | 4.48e-33 | 312 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
| GO:004316112 | Liver | Cirrhotic | proteasome-mediated ubiquitin-dependent protein catabolic process | 184/4634 | 412/18723 | 4.52e-19 | 8.85e-17 | 184 |
| GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
| GO:004316122 | Liver | HCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 299/7958 | 412/18723 | 7.82e-36 | 8.27e-33 | 299 |
| GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:004316120 | Oral cavity | OSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 285/7305 | 412/18723 | 5.68e-36 | 5.99e-33 | 285 |
| GO:0010498110 | Oral cavity | LP | proteasomal protein catabolic process | 224/4623 | 490/18723 | 9.57e-25 | 4.00e-22 | 224 |
| GO:0043161110 | Oral cavity | LP | proteasome-mediated ubiquitin-dependent protein catabolic process | 190/4623 | 412/18723 | 1.08e-21 | 2.93e-19 | 190 |
| GO:001049828 | Skin | cSCC | proteasomal protein catabolic process | 243/4864 | 490/18723 | 7.85e-30 | 4.10e-27 | 243 |
| GO:004316128 | Skin | cSCC | proteasome-mediated ubiquitin-dependent protein catabolic process | 205/4864 | 412/18723 | 1.46e-25 | 4.16e-23 | 205 |
| GO:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
| GO:0043161113 | Thyroid | PTC | proteasome-mediated ubiquitin-dependent protein catabolic process | 254/5968 | 412/18723 | 3.91e-36 | 4.54e-33 | 254 |
| GO:001049832 | Thyroid | ATC | proteasomal protein catabolic process | 309/6293 | 490/18723 | 1.78e-41 | 1.13e-37 | 309 |
| GO:0043161210 | Thyroid | ATC | proteasome-mediated ubiquitin-dependent protein catabolic process | 265/6293 | 412/18723 | 7.09e-38 | 1.49e-34 | 265 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501239 | Esophagus | HGIN | Parkinson disease | 124/1383 | 266/8465 | 5.95e-32 | 9.70e-30 | 7.70e-30 | 124 |
| hsa0501630 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa0502030 | Esophagus | HGIN | Prion disease | 117/1383 | 273/8465 | 4.15e-26 | 3.38e-24 | 2.69e-24 | 117 |
| hsa0501430 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
| hsa0502230 | Esophagus | HGIN | Pathways of neurodegeneration - multiple diseases | 153/1383 | 476/8465 | 1.22e-18 | 4.41e-17 | 3.50e-17 | 153 |
| hsa0501030 | Esophagus | HGIN | Alzheimer disease | 130/1383 | 384/8465 | 5.26e-18 | 1.71e-16 | 1.36e-16 | 130 |
| hsa0305027 | Esophagus | HGIN | Proteasome | 34/1383 | 46/8465 | 6.45e-18 | 1.91e-16 | 1.52e-16 | 34 |
| hsa0501727 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
| hsa0516930 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
| hsa05012114 | Esophagus | HGIN | Parkinson disease | 124/1383 | 266/8465 | 5.95e-32 | 9.70e-30 | 7.70e-30 | 124 |
| hsa05016113 | Esophagus | HGIN | Huntington disease | 129/1383 | 306/8465 | 6.81e-28 | 7.41e-26 | 5.88e-26 | 129 |
| hsa05020113 | Esophagus | HGIN | Prion disease | 117/1383 | 273/8465 | 4.15e-26 | 3.38e-24 | 2.69e-24 | 117 |
| hsa05014113 | Esophagus | HGIN | Amyotrophic lateral sclerosis | 140/1383 | 364/8465 | 2.13e-25 | 1.16e-23 | 9.19e-24 | 140 |
| hsa05022113 | Esophagus | HGIN | Pathways of neurodegeneration - multiple diseases | 153/1383 | 476/8465 | 1.22e-18 | 4.41e-17 | 3.50e-17 | 153 |
| hsa05010113 | Esophagus | HGIN | Alzheimer disease | 130/1383 | 384/8465 | 5.26e-18 | 1.71e-16 | 1.36e-16 | 130 |
| hsa03050111 | Esophagus | HGIN | Proteasome | 34/1383 | 46/8465 | 6.45e-18 | 1.91e-16 | 1.52e-16 | 34 |
| hsa05017112 | Esophagus | HGIN | Spinocerebellar ataxia | 43/1383 | 143/8465 | 2.68e-05 | 3.64e-04 | 2.89e-04 | 43 |
| hsa05169114 | Esophagus | HGIN | Epstein-Barr virus infection | 55/1383 | 202/8465 | 5.13e-05 | 6.19e-04 | 4.92e-04 | 55 |
| hsa05014210 | Esophagus | ESCC | Amyotrophic lateral sclerosis | 266/4205 | 364/8465 | 1.31e-20 | 2.20e-18 | 1.13e-18 | 266 |
| hsa05016210 | Esophagus | ESCC | Huntington disease | 226/4205 | 306/8465 | 1.38e-18 | 8.72e-17 | 4.46e-17 | 226 |
| Page: 1 2 3 4 5 6 |
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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 |
| PSMD6 | SNV | Missense_Mutation | c.742A>C | p.Lys248Gln | p.K248Q | Q15008 | protein_coding | deleterious(0.01) | possibly_damaging(0.714) | TCGA-B6-A0RS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PSMD6 | SNV | Missense_Mutation | c.958N>T | p.Arg320Cys | p.R320C | Q15008 | protein_coding | deleterious(0.01) | probably_damaging(0.935) | TCGA-C8-A1HN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PSMD6 | SNV | Missense_Mutation | c.57N>G | p.Ile19Met | p.I19M | Q15008 | protein_coding | deleterious(0.03) | possibly_damaging(0.772) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD6 | SNV | Missense_Mutation | rs757884032 | c.94N>T | p.Arg32Cys | p.R32C | Q15008 | protein_coding | deleterious_low_confidence(0) | benign(0.416) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMD6 | SNV | Missense_Mutation | c.695N>A | p.Arg232His | p.R232H | Q15008 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD6 | SNV | Missense_Mutation | rs748146502 | c.694N>T | p.Arg232Cys | p.R232C | Q15008 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-4107-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | 5 | SD |
| PSMD6 | SNV | Missense_Mutation | c.733N>T | p.Arg245Cys | p.R245C | Q15008 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PSMD6 | SNV | Missense_Mutation | c.865N>T | p.Leu289Phe | p.L289F | Q15008 | protein_coding | deleterious(0.01) | probably_damaging(0.957) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD6 | SNV | Missense_Mutation | novel | c.460N>T | p.Arg154Cys | p.R154C | Q15008 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PSMD6 | SNV | Missense_Mutation | novel | c.374N>G | p.Lys125Arg | p.K125R | Q15008 | protein_coding | tolerated(0.64) | benign(0.007) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
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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 |
| 9861 | PSMD6 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 9861 | PSMD6 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 9861 | PSMD6 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 9861 | PSMD6 | NA | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 9861 | PSMD6 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 9861 | PSMD6 | NA | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 9861 | PSMD6 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 9861 | PSMD6 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB |
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