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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 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501437 | Oral cavity | LP | Amyotrophic lateral sclerosis | 197/2418 | 364/8465 | 1.25e-25 | 1.39e-23 | 8.93e-24 | 197 |
hsa0501637 | Oral cavity | LP | Huntington disease | 172/2418 | 306/8465 | 6.31e-25 | 5.25e-23 | 3.39e-23 | 172 |
hsa0501037 | Oral cavity | LP | Alzheimer disease | 197/2418 | 384/8465 | 6.66e-22 | 3.69e-20 | 2.38e-20 | 197 |
hsa0502237 | Oral cavity | LP | Pathways of neurodegeneration - multiple diseases | 232/2418 | 476/8465 | 7.77e-22 | 3.69e-20 | 2.38e-20 | 232 |
hsa0502037 | Oral cavity | LP | Prion disease | 149/2418 | 273/8465 | 4.88e-20 | 1.81e-18 | 1.16e-18 | 149 |
hsa0305036 | Oral cavity | LP | Proteasome | 41/2418 | 46/8465 | 1.05e-17 | 3.17e-16 | 2.05e-16 | 41 |
hsa0516936 | Oral cavity | LP | Epstein-Barr virus infection | 106/2418 | 202/8465 | 4.30e-13 | 9.54e-12 | 6.15e-12 | 106 |
hsa0501735 | Oral cavity | LP | Spinocerebellar ataxia | 59/2418 | 143/8465 | 6.97e-04 | 3.46e-03 | 2.23e-03 | 59 |
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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 |
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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. |
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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 |
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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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