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Gene: PSME3 |
Gene summary for PSME3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSME3 | Gene ID | 10197 |
| Gene name | proteasome activator subunit 3 | |
| Gene Alias | HEL-S-283 | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0000082 | UniProtAcc | A0A024R203 |
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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 |
| 10197 | PSME3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 4.88e-04 | 3.65e-01 | -0.0811 |
| 10197 | PSME3 | HTA11_347_2000001011 | Human | Colorectum | AD | 6.98e-10 | 3.50e-01 | -0.1954 |
| 10197 | PSME3 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.35e-02 | 3.54e-01 | -0.1526 |
| 10197 | PSME3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 7.54e-05 | 3.66e-01 | -0.059 |
| 10197 | PSME3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 7.66e-05 | 5.28e-01 | -0.1706 |
| 10197 | PSME3 | HTA11_6801_2000001011 | Human | Colorectum | SER | 4.85e-05 | 5.45e-01 | 0.0171 |
| 10197 | PSME3 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.94e-02 | 2.23e-01 | 0.0674 |
| 10197 | PSME3 | HTA11_7469_2000001011 | Human | Colorectum | AD | 4.74e-05 | 5.26e-01 | -0.0124 |
| 10197 | PSME3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.17e-04 | 3.02e-01 | 0.294 |
| 10197 | PSME3 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.09e-02 | 8.11e-01 | 0.3487 |
| 10197 | PSME3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.90e-16 | 6.58e-01 | 0.281 |
| 10197 | PSME3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.96e-21 | 6.35e-01 | 0.3859 |
| 10197 | PSME3 | LZE4T | Human | Esophagus | ESCC | 2.15e-13 | 3.71e-01 | 0.0811 |
| 10197 | PSME3 | LZE7T | Human | Esophagus | ESCC | 5.33e-06 | 5.75e-01 | 0.0667 |
| 10197 | PSME3 | LZE8T | Human | Esophagus | ESCC | 7.36e-06 | 2.44e-01 | 0.067 |
| 10197 | PSME3 | LZE20T | Human | Esophagus | ESCC | 7.35e-07 | 7.22e-02 | 0.0662 |
| 10197 | PSME3 | LZE22T | Human | Esophagus | ESCC | 9.00e-04 | 2.67e-01 | 0.068 |
| 10197 | PSME3 | LZE24T | Human | Esophagus | ESCC | 5.12e-25 | 6.60e-01 | 0.0596 |
| 10197 | PSME3 | LZE21T | Human | Esophagus | ESCC | 5.02e-06 | 2.90e-01 | 0.0655 |
| 10197 | PSME3 | LZE6T | Human | Esophagus | ESCC | 5.39e-06 | 3.30e-01 | 0.0845 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:00109522 | Colorectum | MSS | positive regulation of peptidase activity | 63/3467 | 197/18723 | 3.65e-06 | 1.06e-04 | 63 |
| GO:00525482 | Colorectum | MSS | regulation of endopeptidase activity | 117/3467 | 432/18723 | 6.25e-06 | 1.65e-04 | 117 |
| GO:00109502 | Colorectum | MSS | positive regulation of endopeptidase activity | 54/3467 | 179/18723 | 1.03e-04 | 1.61e-03 | 54 |
| GO:00971912 | Colorectum | MSS | extrinsic apoptotic signaling pathway | 63/3467 | 219/18723 | 1.34e-04 | 2.03e-03 | 63 |
| GO:20012371 | Colorectum | MSS | negative regulation of extrinsic apoptotic signaling pathway | 30/3467 | 97/18723 | 2.15e-03 | 1.80e-02 | 30 |
| GO:20012361 | Colorectum | MSS | regulation of extrinsic apoptotic signaling pathway | 42/3467 | 151/18723 | 3.23e-03 | 2.45e-02 | 42 |
| GO:00073461 | Colorectum | MSS | regulation of mitotic cell cycle | 108/3467 | 457/18723 | 3.30e-03 | 2.50e-02 | 108 |
| GO:00421763 | Colorectum | MSI-H | regulation of protein catabolic process | 65/1319 | 391/18723 | 6.96e-11 | 1.29e-08 | 65 |
| GO:20012333 | Colorectum | MSI-H | regulation of apoptotic signaling pathway | 61/1319 | 356/18723 | 7.62e-11 | 1.37e-08 | 61 |
| GO:19033623 | Colorectum | MSI-H | regulation of cellular protein catabolic process | 49/1319 | 255/18723 | 9.82e-11 | 1.66e-08 | 49 |
| GO:19030503 | Colorectum | MSI-H | regulation of proteolysis involved in cellular protein catabolic process | 43/1319 | 221/18723 | 9.16e-10 | 1.27e-07 | 43 |
| GO:00104983 | Colorectum | MSI-H | proteasomal protein catabolic process | 71/1319 | 490/18723 | 4.67e-09 | 6.03e-07 | 71 |
| GO:20012343 | Colorectum | MSI-H | negative regulation of apoptotic signaling pathway | 41/1319 | 224/18723 | 1.43e-08 | 1.69e-06 | 41 |
| GO:00525473 | Colorectum | MSI-H | regulation of peptidase activity | 66/1319 | 461/18723 | 2.63e-08 | 2.81e-06 | 66 |
| GO:00611363 | Colorectum | MSI-H | regulation of proteasomal protein catabolic process | 34/1319 | 187/18723 | 2.84e-07 | 2.25e-05 | 34 |
| GO:00525483 | Colorectum | MSI-H | regulation of endopeptidase activity | 60/1319 | 432/18723 | 3.29e-07 | 2.57e-05 | 60 |
| GO:00458623 | Colorectum | MSI-H | positive regulation of proteolysis | 49/1319 | 372/18723 | 1.67e-05 | 7.15e-04 | 49 |
| GO:00109523 | Colorectum | MSI-H | positive regulation of peptidase activity | 28/1319 | 197/18723 | 2.97e-04 | 7.27e-03 | 28 |
| GO:20012372 | Colorectum | MSI-H | negative regulation of extrinsic apoptotic signaling pathway | 15/1319 | 97/18723 | 3.15e-03 | 3.91e-02 | 15 |
| GO:00971913 | Colorectum | MSI-H | extrinsic apoptotic signaling pathway | 27/1319 | 219/18723 | 3.22e-03 | 3.97e-02 | 27 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa03050 | Colorectum | AD | Proteasome | 29/2092 | 46/8465 | 3.87e-08 | 6.18e-07 | 3.94e-07 | 29 |
| hsa05160 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
| hsa030501 | Colorectum | AD | Proteasome | 29/2092 | 46/8465 | 3.87e-08 | 6.18e-07 | 3.94e-07 | 29 |
| hsa051601 | Colorectum | AD | Hepatitis C | 54/2092 | 157/8465 | 3.87e-03 | 1.96e-02 | 1.25e-02 | 54 |
| hsa04612 | Colorectum | SER | Antigen processing and presentation | 25/1580 | 78/8465 | 3.11e-03 | 2.11e-02 | 1.53e-02 | 25 |
| hsa046121 | Colorectum | SER | Antigen processing and presentation | 25/1580 | 78/8465 | 3.11e-03 | 2.11e-02 | 1.53e-02 | 25 |
| hsa030504 | Colorectum | MSS | Proteasome | 29/1875 | 46/8465 | 2.72e-09 | 5.69e-08 | 3.48e-08 | 29 |
| hsa051602 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
| hsa046122 | Colorectum | MSS | Antigen processing and presentation | 27/1875 | 78/8465 | 7.72e-03 | 2.91e-02 | 1.78e-02 | 27 |
| hsa030505 | Colorectum | MSS | Proteasome | 29/1875 | 46/8465 | 2.72e-09 | 5.69e-08 | 3.48e-08 | 29 |
| hsa051603 | Colorectum | MSS | Hepatitis C | 52/1875 | 157/8465 | 9.29e-04 | 5.58e-03 | 3.42e-03 | 52 |
| hsa046123 | Colorectum | MSS | Antigen processing and presentation | 27/1875 | 78/8465 | 7.72e-03 | 2.91e-02 | 1.78e-02 | 27 |
| hsa046124 | Colorectum | MSI-H | Antigen processing and presentation | 23/797 | 78/8465 | 4.15e-07 | 7.91e-06 | 6.63e-06 | 23 |
| hsa046125 | Colorectum | MSI-H | Antigen processing and presentation | 23/797 | 78/8465 | 4.15e-07 | 7.91e-06 | 6.63e-06 | 23 |
| hsa0305028 | Esophagus | ESCC | Proteasome | 44/4205 | 46/8465 | 1.05e-11 | 1.60e-10 | 8.21e-11 | 44 |
| hsa051609 | Esophagus | ESCC | Hepatitis C | 107/4205 | 157/8465 | 1.75e-06 | 1.08e-05 | 5.55e-06 | 107 |
| hsa0461230 | Esophagus | ESCC | Antigen processing and presentation | 51/4205 | 78/8465 | 3.57e-03 | 9.34e-03 | 4.78e-03 | 51 |
| hsa0305037 | Esophagus | ESCC | Proteasome | 44/4205 | 46/8465 | 1.05e-11 | 1.60e-10 | 8.21e-11 | 44 |
| hsa0516016 | Esophagus | ESCC | Hepatitis C | 107/4205 | 157/8465 | 1.75e-06 | 1.08e-05 | 5.55e-06 | 107 |
| hsa04612114 | Esophagus | ESCC | Antigen processing and presentation | 51/4205 | 78/8465 | 3.57e-03 | 9.34e-03 | 4.78e-03 | 51 |
| Page: 1 2 |
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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 |
| PSME3 | SNV | Missense_Mutation | rs751193290 | c.691N>T | p.Arg231Trp | p.R231W | P61289 | protein_coding | tolerated(0.23) | probably_damaging(0.942) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| PSME3 | SNV | Missense_Mutation | rs751193290 | c.691C>T | p.Arg231Trp | p.R231W | P61289 | protein_coding | tolerated(0.23) | probably_damaging(0.942) | TCGA-DS-A0VN-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PSME3 | SNV | Missense_Mutation | rs751193290 | c.691N>T | p.Arg231Trp | p.R231W | P61289 | protein_coding | tolerated(0.23) | probably_damaging(0.942) | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| PSME3 | SNV | Missense_Mutation | c.431N>A | p.Cys144Tyr | p.C144Y | P61289 | protein_coding | tolerated_low_confidence(0.12) | benign(0) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| PSME3 | SNV | Missense_Mutation | c.620N>A | p.Ala207Asp | p.A207D | P61289 | protein_coding | deleterious(0) | possibly_damaging(0.884) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSME3 | SNV | Missense_Mutation | rs767374760 | c.404N>T | p.Thr135Met | p.T135M | P61289 | protein_coding | tolerated(0.23) | probably_damaging(0.917) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| PSME3 | SNV | Missense_Mutation | rs751193290 | c.691N>T | p.Arg231Trp | p.R231W | P61289 | protein_coding | tolerated(0.23) | probably_damaging(0.942) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSME3 | SNV | Missense_Mutation | novel | c.650G>A | p.Arg217His | p.R217H | P61289 | protein_coding | deleterious(0) | benign(0.165) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSME3 | SNV | Missense_Mutation | rs763446052 | c.379N>T | p.Arg127Trp | p.R127W | P61289 | protein_coding | deleterious(0.05) | probably_damaging(0.941) | TCGA-E6-A1LX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PSME3 | SNV | Missense_Mutation | novel | c.596N>A | p.Arg199Lys | p.R199K | P61289 | protein_coding | deleterious(0.03) | benign(0.022) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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 |
| 10197 | PSME3 | NA | inhibitor | BORTEZOMIB | BORTEZOMIB | |
| 10197 | PSME3 | NA | inhibitor | CARFILZOMIB | CARFILZOMIB |
| Page: 1 |
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