|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PSMD4 |
Gene summary for PSMD4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMD4 | Gene ID | 5710 |
| Gene name | proteasome 26S subunit ubiquitin receptor, non-ATPase 4 | |
| Gene Alias | AF | |
| Cytomap | 1q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | Q5VWC4 |
Top |
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 |
| 5710 | PSMD4 | GSM4909285 | Human | Breast | IDC | 3.85e-10 | 4.60e-01 | 0.21 |
| 5710 | PSMD4 | GSM4909296 | Human | Breast | IDC | 1.38e-07 | 8.03e-02 | 0.1524 |
| 5710 | PSMD4 | GSM4909297 | Human | Breast | IDC | 8.33e-10 | -2.37e-02 | 0.1517 |
| 5710 | PSMD4 | GSM4909301 | Human | Breast | IDC | 8.24e-05 | -2.31e-01 | 0.1577 |
| 5710 | PSMD4 | GSM4909306 | Human | Breast | IDC | 5.26e-03 | 2.99e-01 | 0.1564 |
| 5710 | PSMD4 | GSM4909308 | Human | Breast | IDC | 4.01e-16 | 5.29e-01 | 0.158 |
| 5710 | PSMD4 | GSM4909311 | Human | Breast | IDC | 1.29e-22 | -1.84e-01 | 0.1534 |
| 5710 | PSMD4 | GSM4909312 | Human | Breast | IDC | 5.87e-08 | 7.11e-02 | 0.1552 |
| 5710 | PSMD4 | GSM4909317 | Human | Breast | IDC | 1.54e-02 | 3.13e-01 | 0.1355 |
| 5710 | PSMD4 | GSM4909319 | Human | Breast | IDC | 3.33e-36 | -6.70e-02 | 0.1563 |
| 5710 | PSMD4 | GSM4909320 | Human | Breast | IDC | 1.69e-05 | -3.26e-02 | 0.1575 |
| 5710 | PSMD4 | GSM4909321 | Human | Breast | IDC | 1.13e-31 | 5.72e-01 | 0.1559 |
| 5710 | PSMD4 | brca1 | Human | Breast | Precancer | 2.29e-12 | 4.58e-01 | -0.0338 |
| 5710 | PSMD4 | brca2 | Human | Breast | Precancer | 3.16e-14 | 4.07e-01 | -0.024 |
| 5710 | PSMD4 | brca3 | Human | Breast | Precancer | 3.99e-09 | 4.16e-01 | -0.0263 |
| 5710 | PSMD4 | M2 | Human | Breast | IDC | 1.77e-05 | 3.89e-01 | 0.21 |
| 5710 | PSMD4 | NCCBC14 | Human | Breast | DCIS | 2.63e-08 | 7.18e-02 | 0.2021 |
| 5710 | PSMD4 | NCCBC5 | Human | Breast | DCIS | 5.66e-13 | 7.96e-02 | 0.2046 |
| 5710 | PSMD4 | P1 | Human | Breast | IDC | 1.75e-16 | -1.31e-01 | 0.1527 |
| 5710 | PSMD4 | P2 | Human | Breast | IDC | 4.51e-05 | 3.46e-01 | 0.21 |
| 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 | ||
| 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. |
Top |
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: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: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:004316124 | Breast | DCIS | proteasome-mediated ubiquitin-dependent protein catabolic process | 57/1390 | 412/18723 | 3.76e-06 | 1.16e-04 | 57 |
| 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: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: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:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
| GO:00431613 | Colorectum | MSI-H | proteasome-mediated ubiquitin-dependent protein catabolic process | 53/1319 | 412/18723 | 1.51e-05 | 6.62e-04 | 53 |
| 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 |
| Page: 1 2 |
| 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 |
Top |
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 |
Top |
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 |
Top |
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 |
| PSMD4 | SNV | Missense_Mutation | rs770584632 | c.1108N>A | p.Gly370Ser | p.G370S | protein_coding | tolerated(0.57) | benign(0.003) | TCGA-AN-A0FZ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PSMD4 | SNV | Missense_Mutation | c.10N>C | p.Glu4Gln | p.E4Q | protein_coding | deleterious(0.03) | benign(0.251) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD | ||
| PSMD4 | deletion | Frame_Shift_Del | novel | c.514delA | p.Thr172GlnfsTer37 | p.T172Qfs*37 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | |||
| PSMD4 | SNV | Missense_Mutation | c.112N>T | p.His38Tyr | p.H38Y | protein_coding | tolerated(0.58) | possibly_damaging(0.516) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PSMD4 | SNV | Missense_Mutation | novel | c.1007N>G | p.Glu336Gly | p.E336G | protein_coding | tolerated(0.15) | benign(0.211) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| PSMD4 | SNV | Missense_Mutation | rs768592153 | c.101N>G | p.Asn34Ser | p.N34S | protein_coding | tolerated(0.24) | possibly_damaging(0.646) | TCGA-A6-6780-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD4 | SNV | Missense_Mutation | c.520N>T | p.Pro174Ser | p.P174S | protein_coding | deleterious(0.02) | probably_damaging(0.951) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | ||
| PSMD4 | SNV | Missense_Mutation | novel | c.132N>A | p.Asn44Lys | p.N44K | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PSMD4 | SNV | Missense_Mutation | rs181572831 | c.823N>T | p.Arg275Cys | p.R275C | protein_coding | deleterious(0.05) | benign(0.228) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PSMD4 | SNV | Missense_Mutation | novel | c.1067N>A | p.Arg356Gln | p.R356Q | protein_coding | tolerated(0.33) | benign(0.121) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 |
Top |
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 |
| 5710 | PSMD4 | NA | PROTEASOME INHIBITOR | 15899868 | ||
| 5710 | PSMD4 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5710 | PSMD4 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5710 | PSMD4 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5710 | PSMD4 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5710 | PSMD4 | NA | TALAZOPARIB | TALAZOPARIB | 28316110 | |
| 5710 | PSMD4 | NA | CARFILZOMIB | CARFILZOMIB | 27033953 | |
| 5710 | PSMD4 | NA | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5710 | PSMD4 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5710 | PSMD4 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 |
| Page: 1 2 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |