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Gene: PUS1 |
Gene summary for PUS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PUS1 | Gene ID | 80324 |
| Gene name | pseudouridine synthase 1 | |
| Gene Alias | MLASA1 | |
| Cytomap | 12q24.33 | |
| Gene Type | protein-coding | GO ID | GO:0000959 | UniProtAcc | E5KMT6 |
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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 |
| 80324 | PUS1 | LZE7T | Human | Esophagus | ESCC | 1.07e-10 | 2.05e-01 | 0.0667 |
| 80324 | PUS1 | LZE22T | Human | Esophagus | ESCC | 5.29e-04 | 3.62e-01 | 0.068 |
| 80324 | PUS1 | LZE24T | Human | Esophagus | ESCC | 2.43e-09 | 1.80e-01 | 0.0596 |
| 80324 | PUS1 | P1T-E | Human | Esophagus | ESCC | 4.08e-07 | 3.20e-01 | 0.0875 |
| 80324 | PUS1 | P2T-E | Human | Esophagus | ESCC | 3.63e-20 | 3.80e-01 | 0.1177 |
| 80324 | PUS1 | P4T-E | Human | Esophagus | ESCC | 1.11e-15 | 3.97e-01 | 0.1323 |
| 80324 | PUS1 | P5T-E | Human | Esophagus | ESCC | 1.22e-21 | 3.30e-01 | 0.1327 |
| 80324 | PUS1 | P8T-E | Human | Esophagus | ESCC | 2.88e-12 | 1.56e-01 | 0.0889 |
| 80324 | PUS1 | P9T-E | Human | Esophagus | ESCC | 5.85e-10 | 2.36e-01 | 0.1131 |
| 80324 | PUS1 | P10T-E | Human | Esophagus | ESCC | 4.48e-14 | 2.19e-01 | 0.116 |
| 80324 | PUS1 | P11T-E | Human | Esophagus | ESCC | 9.09e-07 | 1.44e-01 | 0.1426 |
| 80324 | PUS1 | P12T-E | Human | Esophagus | ESCC | 8.06e-07 | 9.65e-02 | 0.1122 |
| 80324 | PUS1 | P15T-E | Human | Esophagus | ESCC | 1.37e-16 | 1.90e-01 | 0.1149 |
| 80324 | PUS1 | P16T-E | Human | Esophagus | ESCC | 1.90e-11 | 1.27e-01 | 0.1153 |
| 80324 | PUS1 | P17T-E | Human | Esophagus | ESCC | 1.25e-05 | 3.22e-01 | 0.1278 |
| 80324 | PUS1 | P19T-E | Human | Esophagus | ESCC | 3.61e-04 | 4.12e-01 | 0.1662 |
| 80324 | PUS1 | P20T-E | Human | Esophagus | ESCC | 4.34e-17 | 2.74e-01 | 0.1124 |
| 80324 | PUS1 | P21T-E | Human | Esophagus | ESCC | 8.40e-18 | 3.63e-01 | 0.1617 |
| 80324 | PUS1 | P22T-E | Human | Esophagus | ESCC | 3.22e-12 | 1.63e-01 | 0.1236 |
| 80324 | PUS1 | P23T-E | Human | Esophagus | ESCC | 3.43e-14 | 3.71e-01 | 0.108 |
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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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:014005313 | Esophagus | ESCC | mitochondrial gene expression | 93/8552 | 108/18723 | 1.96e-18 | 2.03e-16 | 93 |
| 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:00009592 | Esophagus | ESCC | mitochondrial RNA metabolic process | 39/8552 | 49/18723 | 1.20e-06 | 1.49e-05 | 39 |
| GO:00009631 | Esophagus | ESCC | mitochondrial RNA processing | 19/8552 | 20/18723 | 3.83e-06 | 4.14e-05 | 19 |
| 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:0090646 | Esophagus | ESCC | mitochondrial tRNA processing | 11/8552 | 12/18723 | 1.26e-03 | 6.06e-03 | 11 |
| 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:01400531 | Liver | HCC | mitochondrial gene expression | 82/7958 | 108/18723 | 1.49e-12 | 7.20e-11 | 82 |
| 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:0000959 | Liver | HCC | mitochondrial RNA metabolic process | 30/7958 | 49/18723 | 6.31e-03 | 2.57e-02 | 30 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
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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. |
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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 |
| PUS1 | SNV | Missense_Mutation | c.731N>G | p.Asn244Ser | p.N244S | Q9Y606 | protein_coding | tolerated(0.05) | possibly_damaging(0.654) | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| PUS1 | SNV | Missense_Mutation | rs573837941 | c.946N>T | p.Arg316Cys | p.R316C | Q9Y606 | protein_coding | deleterious(0.03) | benign(0.117) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| PUS1 | SNV | Missense_Mutation | c.769C>T | p.Pro257Ser | p.P257S | Q9Y606 | protein_coding | deleterious(0) | possibly_damaging(0.904) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| PUS1 | SNV | Missense_Mutation | rs750169475 | c.1037N>A | p.Arg346His | p.R346H | Q9Y606 | protein_coding | deleterious(0) | probably_damaging(0.985) | TCGA-BH-A1F2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| PUS1 | SNV | Missense_Mutation | novel | c.1252N>A | p.Glu418Lys | p.E418K | Q9Y606 | protein_coding | tolerated(0.18) | benign(0.005) | TCGA-EA-A3HS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PUS1 | SNV | Missense_Mutation | c.658G>A | p.Glu220Lys | p.E220K | Q9Y606 | protein_coding | tolerated(0.11) | benign(0.017) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PUS1 | SNV | Missense_Mutation | rs371146708 | c.782N>A | p.Arg261His | p.R261H | Q9Y606 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-6651-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Ancillary | leucovorin | SD |
| PUS1 | SNV | Missense_Mutation | c.401N>C | p.Met134Thr | p.M134T | Q9Y606 | protein_coding | tolerated(0.06) | benign(0.27) | TCGA-AA-3966-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PUS1 | SNV | Missense_Mutation | rs376680579 | c.676N>A | p.Ala226Thr | p.A226T | Q9Y606 | protein_coding | tolerated(0.56) | benign(0.003) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| PUS1 | SNV | Missense_Mutation | rs148218985 | c.1096N>A | p.Ala366Thr | p.A366T | Q9Y606 | protein_coding | tolerated(0.46) | benign(0.001) | TCGA-D5-6533-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | oxaliplatin | CR |
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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 |
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