|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: PSMA4 |
Gene summary for PSMA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMA4 | Gene ID | 5685 |
| Gene name | proteasome 20S subunit alpha 4 | |
| Gene Alias | HC9 | |
| Cytomap | 15q25.1 | |
| Gene Type | protein-coding | GO ID | GO:0006508 | UniProtAcc | P25789 |
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 |
| 5685 | PSMA4 | GSM4909282 | Human | Breast | IDC | 5.77e-11 | 4.25e-01 | -0.0288 |
| 5685 | PSMA4 | GSM4909286 | Human | Breast | IDC | 8.30e-03 | -1.34e-01 | 0.1081 |
| 5685 | PSMA4 | GSM4909287 | Human | Breast | IDC | 4.94e-17 | 4.89e-01 | 0.2057 |
| 5685 | PSMA4 | GSM4909290 | Human | Breast | IDC | 1.62e-02 | 3.22e-01 | 0.2096 |
| 5685 | PSMA4 | GSM4909296 | Human | Breast | IDC | 1.52e-06 | -6.15e-02 | 0.1524 |
| 5685 | PSMA4 | GSM4909297 | Human | Breast | IDC | 1.20e-15 | -3.42e-02 | 0.1517 |
| 5685 | PSMA4 | GSM4909301 | Human | Breast | IDC | 4.22e-08 | -3.37e-01 | 0.1577 |
| 5685 | PSMA4 | GSM4909302 | Human | Breast | IDC | 2.10e-07 | -4.01e-01 | 0.1545 |
| 5685 | PSMA4 | GSM4909308 | Human | Breast | IDC | 5.64e-04 | 3.05e-01 | 0.158 |
| 5685 | PSMA4 | GSM4909311 | Human | Breast | IDC | 1.18e-33 | -4.66e-01 | 0.1534 |
| 5685 | PSMA4 | GSM4909312 | Human | Breast | IDC | 5.33e-09 | -1.66e-01 | 0.1552 |
| 5685 | PSMA4 | GSM4909313 | Human | Breast | IDC | 2.08e-08 | -3.91e-01 | 0.0391 |
| 5685 | PSMA4 | GSM4909319 | Human | Breast | IDC | 1.69e-37 | -4.54e-01 | 0.1563 |
| 5685 | PSMA4 | GSM4909320 | Human | Breast | IDC | 2.44e-06 | -4.97e-01 | 0.1575 |
| 5685 | PSMA4 | GSM4909321 | Human | Breast | IDC | 9.17e-15 | -2.99e-02 | 0.1559 |
| 5685 | PSMA4 | brca1 | Human | Breast | Precancer | 2.75e-15 | 5.27e-01 | -0.0338 |
| 5685 | PSMA4 | brca2 | Human | Breast | Precancer | 2.86e-25 | 5.64e-01 | -0.024 |
| 5685 | PSMA4 | brca3 | Human | Breast | Precancer | 2.06e-08 | 3.53e-01 | -0.0263 |
| 5685 | PSMA4 | M2 | Human | Breast | IDC | 2.58e-03 | 1.58e-01 | 0.21 |
| 5685 | PSMA4 | NCCBC14 | Human | Breast | DCIS | 3.87e-11 | -2.70e-02 | 0.2021 |
| 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 | ||
| 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. |
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:001049814 | Breast | IDC | proteasomal protein catabolic process | 75/1434 | 490/18723 | 5.59e-09 | 4.41e-07 | 75 |
| GO:001049824 | Breast | DCIS | proteasomal protein catabolic process | 75/1390 | 490/18723 | 1.44e-09 | 1.40e-07 | 75 |
| GO:001049816 | Endometrium | AEH | proteasomal protein catabolic process | 108/2100 | 490/18723 | 2.73e-12 | 4.67e-10 | 108 |
| GO:001049817 | Endometrium | EEC | proteasomal protein catabolic process | 112/2168 | 490/18723 | 6.99e-13 | 1.40e-10 | 112 |
| GO:001049826 | Esophagus | HGIN | proteasomal protein catabolic process | 139/2587 | 490/18723 | 1.20e-17 | 3.41e-15 | 139 |
| GO:0010498111 | Esophagus | ESCC | proteasomal protein catabolic process | 369/8552 | 490/18723 | 1.13e-41 | 1.80e-38 | 369 |
| GO:001049812 | Liver | Cirrhotic | proteasomal protein catabolic process | 216/4634 | 490/18723 | 2.52e-21 | 9.29e-19 | 216 |
| GO:001049822 | Liver | HCC | proteasomal protein catabolic process | 351/7958 | 490/18723 | 6.92e-40 | 1.46e-36 | 351 |
| GO:001049820 | Oral cavity | OSCC | proteasomal protein catabolic process | 336/7305 | 490/18723 | 5.45e-41 | 8.63e-38 | 336 |
| GO:0010498110 | Oral cavity | LP | proteasomal protein catabolic process | 224/4623 | 490/18723 | 9.57e-25 | 4.00e-22 | 224 |
| GO:001049818 | Prostate | BPH | proteasomal protein catabolic process | 153/3107 | 490/18723 | 4.13e-16 | 7.51e-14 | 153 |
| GO:001049819 | Prostate | Tumor | proteasomal protein catabolic process | 158/3246 | 490/18723 | 3.05e-16 | 6.76e-14 | 158 |
| GO:001049827 | Skin | AK | proteasomal protein catabolic process | 97/1910 | 490/18723 | 9.65e-11 | 1.54e-08 | 97 |
| GO:001049828 | Skin | cSCC | proteasomal protein catabolic process | 243/4864 | 490/18723 | 7.85e-30 | 4.10e-27 | 243 |
| GO:0010498113 | Thyroid | PTC | proteasomal protein catabolic process | 297/5968 | 490/18723 | 4.58e-40 | 9.63e-37 | 297 |
| GO:001049832 | Thyroid | ATC | proteasomal protein catabolic process | 309/6293 | 490/18723 | 1.78e-41 | 1.13e-37 | 309 |
| Page: 1 |
| 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 |
| 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 |
| 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 |
| hsa0501623 | Breast | IDC | Huntington disease | 103/867 | 306/8465 | 5.14e-30 | 4.17e-28 | 3.12e-28 | 103 |
| hsa0501023 | Breast | IDC | Alzheimer disease | 107/867 | 384/8465 | 1.70e-23 | 7.88e-22 | 5.90e-22 | 107 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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 |
| PSMA4 | SNV | Missense_Mutation | c.313N>G | p.Ile105Val | p.I105V | P25789 | protein_coding | tolerated(0.08) | benign(0.127) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| PSMA4 | SNV | Missense_Mutation | novel | c.178T>C | p.Phe60Leu | p.F60L | P25789 | protein_coding | tolerated(0.66) | benign(0.001) | TCGA-E9-A6HE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | CR |
| PSMA4 | deletion | Frame_Shift_Del | novel | c.663delN | p.Lys222ArgfsTer3 | p.K222Rfs*3 | P25789 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| PSMA4 | SNV | Missense_Mutation | rs754693970 | c.746N>A | p.Arg249His | p.R249H | P25789 | protein_coding | tolerated(0.1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSMA4 | SNV | Missense_Mutation | rs751350183 | c.745N>T | p.Arg249Cys | p.R249C | P25789 | protein_coding | deleterious(0.04) | benign(0.106) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PSMA4 | SNV | Missense_Mutation | c.383N>A | p.Arg128His | p.R128H | P25789 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| PSMA4 | SNV | Missense_Mutation | novel | c.750G>T | p.Glu250Asp | p.E250D | P25789 | protein_coding | tolerated(0.18) | possibly_damaging(0.568) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMA4 | SNV | Missense_Mutation | rs147984456 | c.338C>T | p.Ala113Val | p.A113V | P25789 | protein_coding | tolerated(0.2) | benign(0.062) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PSMA4 | SNV | Missense_Mutation | novel | c.194N>A | p.Ile65Asn | p.I65N | P25789 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| PSMA4 | SNV | Missense_Mutation | novel | c.754A>G | p.Lys252Glu | p.K252E | P25789 | protein_coding | tolerated(0.49) | possibly_damaging(0.899) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| Page: 1 2 3 |
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 |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL2103884 | OPROZOMIB | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | cotinine | COTININE | ||
| 5685 | PSMA4 | DRUGGABLE GENOME, PROTEASE | inhibitor | CHEMBL371405 | MARIZOMIB |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |