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Gene: PUS3 |
Gene summary for PUS3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PUS3 | Gene ID | 83480 |
| Gene name | pseudouridine synthase 3 | |
| Gene Alias | 2610020J05Rik | |
| Cytomap | 11q24.2 | |
| Gene Type | protein-coding | GO ID | GO:0001522 | UniProtAcc | A0A087WY59 |
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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 |
| 83480 | PUS3 | LZE4T | Human | Esophagus | ESCC | 3.28e-04 | 1.31e-01 | 0.0811 |
| 83480 | PUS3 | LZE24T | Human | Esophagus | ESCC | 3.72e-12 | 3.56e-01 | 0.0596 |
| 83480 | PUS3 | P2T-E | Human | Esophagus | ESCC | 4.78e-08 | 9.96e-02 | 0.1177 |
| 83480 | PUS3 | P4T-E | Human | Esophagus | ESCC | 3.61e-18 | 4.94e-01 | 0.1323 |
| 83480 | PUS3 | P5T-E | Human | Esophagus | ESCC | 2.25e-11 | 1.93e-01 | 0.1327 |
| 83480 | PUS3 | P8T-E | Human | Esophagus | ESCC | 2.58e-10 | 5.51e-02 | 0.0889 |
| 83480 | PUS3 | P9T-E | Human | Esophagus | ESCC | 2.06e-03 | 1.37e-01 | 0.1131 |
| 83480 | PUS3 | P10T-E | Human | Esophagus | ESCC | 4.17e-13 | 1.04e-01 | 0.116 |
| 83480 | PUS3 | P11T-E | Human | Esophagus | ESCC | 1.54e-04 | 2.37e-01 | 0.1426 |
| 83480 | PUS3 | P12T-E | Human | Esophagus | ESCC | 2.49e-06 | 1.35e-01 | 0.1122 |
| 83480 | PUS3 | P15T-E | Human | Esophagus | ESCC | 7.84e-04 | 9.22e-02 | 0.1149 |
| 83480 | PUS3 | P16T-E | Human | Esophagus | ESCC | 1.18e-09 | 1.96e-01 | 0.1153 |
| 83480 | PUS3 | P20T-E | Human | Esophagus | ESCC | 7.49e-05 | 6.24e-02 | 0.1124 |
| 83480 | PUS3 | P21T-E | Human | Esophagus | ESCC | 8.46e-12 | 1.55e-01 | 0.1617 |
| 83480 | PUS3 | P22T-E | Human | Esophagus | ESCC | 3.32e-08 | 3.10e-02 | 0.1236 |
| 83480 | PUS3 | P23T-E | Human | Esophagus | ESCC | 1.43e-10 | 2.85e-01 | 0.108 |
| 83480 | PUS3 | P26T-E | Human | Esophagus | ESCC | 5.62e-25 | 4.55e-01 | 0.1276 |
| 83480 | PUS3 | P27T-E | Human | Esophagus | ESCC | 1.13e-08 | 7.66e-02 | 0.1055 |
| 83480 | PUS3 | P30T-E | Human | Esophagus | ESCC | 1.91e-10 | 3.32e-01 | 0.137 |
| 83480 | PUS3 | P31T-E | Human | Esophagus | ESCC | 1.06e-14 | 2.87e-01 | 0.1251 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:00080333 | Esophagus | ESCC | tRNA processing | 92/8552 | 127/18723 | 7.83e-10 | 1.93e-08 | 92 |
| GO:00063992 | Esophagus | ESCC | tRNA metabolic process | 122/8552 | 179/18723 | 9.03e-10 | 2.19e-08 | 122 |
| GO:00094512 | Esophagus | ESCC | RNA modification | 114/8552 | 167/18723 | 2.76e-09 | 6.04e-08 | 114 |
| GO:00064002 | Esophagus | ESCC | tRNA modification | 62/8552 | 90/18723 | 7.02e-06 | 7.04e-05 | 62 |
| GO:00015221 | Esophagus | ESCC | pseudouridine synthesis | 16/8552 | 18/18723 | 1.78e-04 | 1.15e-03 | 16 |
| GO:00165561 | Esophagus | ESCC | mRNA modification | 21/8552 | 27/18723 | 6.88e-04 | 3.61e-03 | 21 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:00346601 | Liver | HCC | ncRNA metabolic process | 332/7958 | 485/18723 | 1.48e-31 | 7.80e-29 | 332 |
| GO:0008033 | Liver | HCC | tRNA processing | 87/7958 | 127/18723 | 2.66e-09 | 7.23e-08 | 87 |
| GO:0006399 | Liver | HCC | tRNA metabolic process | 108/7958 | 179/18723 | 1.07e-06 | 1.59e-05 | 108 |
| GO:0009451 | Liver | HCC | RNA modification | 101/7958 | 167/18723 | 2.02e-06 | 2.78e-05 | 101 |
| GO:0006400 | Liver | HCC | tRNA modification | 60/7958 | 90/18723 | 3.09e-06 | 4.09e-05 | 60 |
| GO:0016556 | Liver | HCC | mRNA modification | 18/7958 | 27/18723 | 9.75e-03 | 3.66e-02 | 18 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| PUS3 | SNV | Missense_Mutation | c.918N>T | p.Glu306Asp | p.E306D | Q9BZE2 | protein_coding | deleterious(0.03) | benign(0.257) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PUS3 | SNV | Missense_Mutation | rs772532957 | c.518N>A | p.Arg173His | p.R173H | Q9BZE2 | protein_coding | deleterious(0) | probably_damaging(0.911) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PUS3 | SNV | Missense_Mutation | novel | c.614N>G | p.Asp205Gly | p.D205G | Q9BZE2 | protein_coding | deleterious(0.01) | possibly_damaging(0.792) | TCGA-VS-A8EK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
| PUS3 | SNV | Missense_Mutation | novel | c.74N>C | p.Val25Ala | p.V25A | Q9BZE2 | protein_coding | tolerated(0.13) | benign(0.11) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PUS3 | SNV | Missense_Mutation | rs201659793 | c.1226N>A | p.Arg409His | p.R409H | Q9BZE2 | protein_coding | deleterious(0) | possibly_damaging(0.615) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
| PUS3 | SNV | Missense_Mutation | rs370110541 | c.586C>T | p.Arg196Cys | p.R196C | Q9BZE2 | protein_coding | deleterious(0) | benign(0.058) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD |
| PUS3 | SNV | Missense_Mutation | rs778490543 | c.273N>T | p.Glu91Asp | p.E91D | Q9BZE2 | protein_coding | tolerated(0.28) | benign(0.27) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PUS3 | SNV | Missense_Mutation | novel | c.102N>C | p.Lys34Asn | p.K34N | Q9BZE2 | protein_coding | tolerated(0.53) | benign(0.001) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PUS3 | SNV | Missense_Mutation | c.925N>T | p.Pro309Ser | p.P309S | Q9BZE2 | protein_coding | deleterious(0.02) | possibly_damaging(0.67) | TCGA-CM-4752-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| PUS3 | SNV | Missense_Mutation | rs201659793 | c.1226N>A | p.Arg409His | p.R409H | Q9BZE2 | protein_coding | deleterious(0) | possibly_damaging(0.615) | TCGA-F4-6856-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Ancillary | leucovorin | CR |
| Page: 1 2 3 4 5 |
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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 |
| Page: 1 |
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