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Gene: PSMD13 |
Gene summary for PSMD13 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSMD13 | Gene ID | 5719 |
| Gene name | proteasome 26S subunit, non-ATPase 13 | |
| Gene Alias | HSPC027 | |
| Cytomap | 11p15.5 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | Q9UNM6 |
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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 |
| 5719 | PSMD13 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.78e-04 | 2.81e-01 | -0.1808 |
| 5719 | PSMD13 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.49e-08 | 4.39e-01 | -0.0811 |
| 5719 | PSMD13 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.46e-12 | 4.20e-01 | -0.1954 |
| 5719 | PSMD13 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.76e-03 | 2.73e-01 | -0.1207 |
| 5719 | PSMD13 | HTA11_696_2000001011 | Human | Colorectum | AD | 7.45e-09 | 3.55e-01 | -0.1464 |
| 5719 | PSMD13 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.34e-07 | 4.03e-01 | -0.059 |
| 5719 | PSMD13 | HTA11_2992_2000001011 | Human | Colorectum | SER | 6.85e-05 | 4.79e-01 | -0.1706 |
| 5719 | PSMD13 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.70e-03 | 2.64e-01 | 0.096 |
| 5719 | PSMD13 | HTA11_6801_2000001011 | Human | Colorectum | SER | 2.57e-02 | 3.90e-01 | 0.0171 |
| 5719 | PSMD13 | HTA11_10711_2000001011 | Human | Colorectum | AD | 8.69e-05 | 3.46e-01 | 0.0338 |
| 5719 | PSMD13 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.32e-14 | 4.32e-01 | 0.0674 |
| 5719 | PSMD13 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.47e-02 | 2.81e-01 | 0.0588 |
| 5719 | PSMD13 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 5.37e-18 | 5.73e-01 | 0.294 |
| 5719 | PSMD13 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.36e-04 | 3.31e-01 | 0.281 |
| 5719 | PSMD13 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 8.64e-23 | 6.98e-01 | 0.3859 |
| 5719 | PSMD13 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.28e-04 | 4.46e-01 | 0.2585 |
| 5719 | PSMD13 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.42e-06 | 2.79e-01 | 0.3005 |
| 5719 | PSMD13 | LZE2T | Human | Esophagus | ESCC | 4.93e-02 | 6.72e-01 | 0.082 |
| 5719 | PSMD13 | LZE4T | Human | Esophagus | ESCC | 6.55e-16 | 4.17e-01 | 0.0811 |
| 5719 | PSMD13 | LZE5T | Human | Esophagus | ESCC | 1.25e-02 | 5.07e-01 | 0.0514 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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. |
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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:00482853 | Esophagus | ESCC | organelle fission | 301/8552 | 488/18723 | 4.64e-13 | 2.12e-11 | 301 |
| GO:00002802 | Esophagus | ESCC | nuclear division | 270/8552 | 439/18723 | 1.17e-11 | 4.24e-10 | 270 |
| GO:0048285 | Liver | HCC | organelle fission | 254/7958 | 488/18723 | 1.07e-05 | 1.23e-04 | 254 |
| GO:0000280 | Liver | HCC | nuclear division | 220/7958 | 439/18723 | 6.90e-04 | 4.25e-03 | 220 |
| GO:00482852 | Oral cavity | OSCC | organelle fission | 265/7305 | 488/18723 | 3.22e-12 | 1.27e-10 | 265 |
| GO:00002801 | Oral cavity | OSCC | nuclear division | 237/7305 | 439/18723 | 9.62e-11 | 2.90e-09 | 237 |
| GO:004828511 | Oral cavity | LP | organelle fission | 145/4623 | 488/18723 | 6.02e-03 | 3.57e-02 | 145 |
| GO:00482854 | Skin | cSCC | organelle fission | 197/4864 | 488/18723 | 1.51e-12 | 8.36e-11 | 197 |
| GO:00002803 | Skin | cSCC | nuclear division | 178/4864 | 439/18723 | 1.17e-11 | 5.93e-10 | 178 |
| GO:00482855 | Thyroid | PTC | organelle fission | 188/5968 | 488/18723 | 9.64e-04 | 5.77e-03 | 188 |
| GO:00002804 | Thyroid | PTC | nuclear division | 167/5968 | 439/18723 | 3.27e-03 | 1.60e-02 | 167 |
| GO:004828512 | Thyroid | ATC | organelle fission | 229/6293 | 488/18723 | 4.79e-10 | 1.29e-08 | 229 |
| GO:000028011 | Thyroid | ATC | nuclear division | 207/6293 | 439/18723 | 1.98e-09 | 4.80e-08 | 207 |
| Page: 1 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05012 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
| hsa05016 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
| hsa05020 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
| hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa03050 | Colorectum | AD | Proteasome | 29/2092 | 46/8465 | 3.87e-08 | 6.18e-07 | 3.94e-07 | 29 |
| hsa05017 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
| hsa050121 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
| hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
| hsa050161 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
| hsa050201 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
| hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
| hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
| hsa030501 | Colorectum | AD | Proteasome | 29/2092 | 46/8465 | 3.87e-08 | 6.18e-07 | 3.94e-07 | 29 |
| hsa050171 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
| hsa050122 | Colorectum | SER | Parkinson disease | 132/1580 | 266/8465 | 2.72e-31 | 9.03e-29 | 6.55e-29 | 132 |
| hsa050202 | Colorectum | SER | Prion disease | 119/1580 | 273/8465 | 4.61e-22 | 3.06e-20 | 2.22e-20 | 119 |
| hsa050162 | Colorectum | SER | Huntington disease | 127/1580 | 306/8465 | 3.29e-21 | 1.37e-19 | 9.92e-20 | 127 |
| hsa050102 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
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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 |
| PSMD13 | SNV | Missense_Mutation | novel | c.429N>T | p.Met143Ile | p.M143I | Q9UNM6 | protein_coding | tolerated(0.46) | benign(0.011) | TCGA-BH-A1EN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PSMD13 | insertion | Nonsense_Mutation | novel | c.985_986insAGTAGCTGCCCCTCTCCCCGTGATGCAGTTGTTGCCTCATTGCA | p.Val329GlufsTer2 | p.V329Efs*2 | Q9UNM6 | protein_coding | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
| PSMD13 | SNV | Missense_Mutation | novel | c.166N>C | p.Glu56Gln | p.E56Q | Q9UNM6 | protein_coding | tolerated(0.48) | benign(0.334) | TCGA-MA-AA3X-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| PSMD13 | SNV | Missense_Mutation | novel | c.506N>A | p.Gly169Glu | p.G169E | Q9UNM6 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| PSMD13 | SNV | Missense_Mutation | c.1079C>T | p.Thr360Met | p.T360M | Q9UNM6 | protein_coding | tolerated(0.09) | possibly_damaging(0.62) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PSMD13 | SNV | Missense_Mutation | rs372085323 | c.382G>A | p.Gly128Arg | p.G128R | Q9UNM6 | protein_coding | tolerated(0.27) | possibly_damaging(0.705) | TCGA-D5-6927-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PSMD13 | SNV | Missense_Mutation | rs746014086 | c.1093A>G | p.Met365Val | p.M365V | Q9UNM6 | protein_coding | tolerated(0.06) | probably_damaging(0.994) | TCGA-QG-A5YV-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | CR |
| PSMD13 | SNV | Missense_Mutation | rs751036999 | c.173N>C | p.Ile58Thr | p.I58T | Q9UNM6 | protein_coding | tolerated(0.09) | benign(0) | TCGA-AG-3909-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | folinic | CR |
| PSMD13 | SNV | Missense_Mutation | novel | c.811N>A | p.Leu271Met | p.L271M | Q9UNM6 | protein_coding | tolerated(0.12) | benign(0.041) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSMD13 | SNV | Missense_Mutation | novel | c.388N>A | p.Leu130Ile | p.L130I | Q9UNM6 | protein_coding | deleterious(0.03) | possibly_damaging(0.513) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
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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 |
| 5719 | PSMD13 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB | |
| 5719 | PSMD13 | NA | inhibitor | CHEMBL325041 | BORTEZOMIB | |
| 5719 | PSMD13 | NA | inhibitor | CHEMBL451887 | CARFILZOMIB | |
| 5719 | PSMD13 | NA | inhibitor | CHEMBL3545432 | IXAZOMIB CITRATE | |
| 5719 | PSMD13 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 5719 | PSMD13 | NA | BORTEZOMIB | BORTEZOMIB | 24524217 | |
| 5719 | PSMD13 | NA | CARFILZOMIB | CARFILZOMIB | 24524217 | |
| 5719 | PSMD13 | NA | inhibitor | CHEMBL2103884 | OPROZOMIB |
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