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Gene: TSR1 |
Gene summary for TSR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TSR1 | Gene ID | 55720 |
| Gene name | TSR1 ribosome maturation factor | |
| Gene Alias | TSR1 | |
| Cytomap | 17p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000462 | UniProtAcc | Q2NL82 |
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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 |
| 55720 | TSR1 | LZE4T | Human | Esophagus | ESCC | 6.21e-15 | 4.31e-01 | 0.0811 |
| 55720 | TSR1 | LZE7T | Human | Esophagus | ESCC | 1.82e-02 | 4.67e-01 | 0.0667 |
| 55720 | TSR1 | LZE8T | Human | Esophagus | ESCC | 3.98e-03 | 1.16e-01 | 0.067 |
| 55720 | TSR1 | LZE22T | Human | Esophagus | ESCC | 6.10e-06 | 2.50e-01 | 0.068 |
| 55720 | TSR1 | LZE24T | Human | Esophagus | ESCC | 1.31e-14 | 4.12e-01 | 0.0596 |
| 55720 | TSR1 | P1T-E | Human | Esophagus | ESCC | 7.90e-06 | 3.09e-01 | 0.0875 |
| 55720 | TSR1 | P2T-E | Human | Esophagus | ESCC | 7.75e-19 | 4.57e-01 | 0.1177 |
| 55720 | TSR1 | P4T-E | Human | Esophagus | ESCC | 1.54e-20 | 6.30e-01 | 0.1323 |
| 55720 | TSR1 | P5T-E | Human | Esophagus | ESCC | 9.73e-12 | 2.94e-01 | 0.1327 |
| 55720 | TSR1 | P8T-E | Human | Esophagus | ESCC | 8.34e-11 | 3.24e-01 | 0.0889 |
| 55720 | TSR1 | P9T-E | Human | Esophagus | ESCC | 1.49e-10 | 4.09e-01 | 0.1131 |
| 55720 | TSR1 | P10T-E | Human | Esophagus | ESCC | 9.59e-13 | 3.36e-01 | 0.116 |
| 55720 | TSR1 | P11T-E | Human | Esophagus | ESCC | 2.81e-08 | 4.69e-01 | 0.1426 |
| 55720 | TSR1 | P12T-E | Human | Esophagus | ESCC | 1.87e-17 | 4.84e-01 | 0.1122 |
| 55720 | TSR1 | P15T-E | Human | Esophagus | ESCC | 3.37e-11 | 2.23e-01 | 0.1149 |
| 55720 | TSR1 | P16T-E | Human | Esophagus | ESCC | 6.53e-26 | 5.95e-01 | 0.1153 |
| 55720 | TSR1 | P17T-E | Human | Esophagus | ESCC | 7.99e-08 | 4.34e-01 | 0.1278 |
| 55720 | TSR1 | P19T-E | Human | Esophagus | ESCC | 1.01e-04 | 1.01e+00 | 0.1662 |
| 55720 | TSR1 | P20T-E | Human | Esophagus | ESCC | 4.92e-08 | 3.45e-01 | 0.1124 |
| 55720 | TSR1 | P21T-E | Human | Esophagus | ESCC | 1.85e-22 | 7.19e-01 | 0.1617 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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:00903052 | Oral cavity | OSCC | nucleic acid phosphodiester bond hydrolysis | 142/7305 | 261/18723 | 2.90e-07 | 4.43e-06 | 142 |
| GO:00004692 | Oral cavity | OSCC | cleavage involved in rRNA processing | 23/7305 | 27/18723 | 1.06e-06 | 1.42e-05 | 23 |
| GO:00004782 | Oral cavity | OSCC | endonucleolytic cleavage involved in rRNA processing | 13/7305 | 15/18723 | 2.07e-04 | 1.36e-03 | 13 |
| GO:00004792 | Oral cavity | OSCC | endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 13/7305 | 15/18723 | 2.07e-04 | 1.36e-03 | 13 |
| GO:00905022 | Oral cavity | OSCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 44/7305 | 82/18723 | 4.95e-03 | 1.94e-02 | 44 |
| GO:002261329 | Skin | cSCC | ribonucleoprotein complex biogenesis | 302/4864 | 463/18723 | 5.13e-72 | 3.22e-68 | 302 |
| GO:004225428 | Skin | cSCC | ribosome biogenesis | 206/4864 | 299/18723 | 3.33e-55 | 1.04e-51 | 206 |
| GO:000636424 | Skin | cSCC | rRNA processing | 156/4864 | 225/18723 | 1.42e-42 | 1.48e-39 | 156 |
| GO:001607224 | Skin | cSCC | rRNA metabolic process | 158/4864 | 236/18723 | 4.06e-40 | 2.83e-37 | 158 |
| GO:003447017 | Skin | cSCC | ncRNA processing | 215/4864 | 395/18723 | 6.83e-34 | 4.28e-31 | 215 |
| GO:003466013 | Skin | cSCC | ncRNA metabolic process | 234/4864 | 485/18723 | 1.37e-26 | 4.77e-24 | 234 |
| GO:004227429 | Skin | cSCC | ribosomal small subunit biogenesis | 59/4864 | 73/18723 | 1.39e-22 | 2.90e-20 | 59 |
| GO:003049012 | Skin | cSCC | maturation of SSU-rRNA | 39/4864 | 50/18723 | 2.04e-14 | 1.40e-12 | 39 |
| GO:000046212 | Skin | cSCC | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 26/4864 | 37/18723 | 2.11e-08 | 6.08e-07 | 26 |
| GO:00905014 | Skin | cSCC | RNA phosphodiester bond hydrolysis | 71/4864 | 152/18723 | 2.72e-08 | 7.41e-07 | 71 |
| GO:00004694 | Skin | cSCC | cleavage involved in rRNA processing | 19/4864 | 27/18723 | 1.72e-06 | 2.88e-05 | 19 |
| GO:00903054 | Skin | cSCC | nucleic acid phosphodiester bond hydrolysis | 97/4864 | 261/18723 | 4.08e-05 | 4.34e-04 | 97 |
| GO:00905024 | Skin | cSCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 34/4864 | 82/18723 | 1.58e-03 | 9.75e-03 | 34 |
| GO:00004784 | Skin | cSCC | endonucleolytic cleavage involved in rRNA processing | 9/4864 | 15/18723 | 5.52e-03 | 2.73e-02 | 9 |
| GO:00004794 | Skin | cSCC | endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 9/4864 | 15/18723 | 5.52e-03 | 2.73e-02 | 9 |
| Page: 1 2 3 4 5 |
| 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 |
| 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 |
| TSR1 | SNV | Missense_Mutation | c.1520N>G | p.Lys507Arg | p.K507R | Q2NL82 | protein_coding | deleterious(0.01) | possibly_damaging(0.819) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TSR1 | SNV | Missense_Mutation | c.1252N>C | p.Glu418Gln | p.E418Q | Q2NL82 | protein_coding | deleterious(0.03) | possibly_damaging(0.548) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TSR1 | SNV | Missense_Mutation | novel | c.1284N>G | p.Asp428Glu | p.D428E | Q2NL82 | protein_coding | tolerated(0.47) | benign(0.007) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TSR1 | SNV | Missense_Mutation | c.1417N>C | p.Glu473Gln | p.E473Q | Q2NL82 | protein_coding | tolerated(0.24) | benign(0.041) | TCGA-AN-A0AM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TSR1 | SNV | Missense_Mutation | rs745709713 | c.1004N>G | p.Asp335Gly | p.D335G | Q2NL82 | protein_coding | tolerated(0.32) | benign(0.001) | TCGA-AQ-A04J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
| TSR1 | SNV | Missense_Mutation | rs750076259 | c.1496N>A | p.Arg499Gln | p.R499Q | Q2NL82 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C8-A26Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TSR1 | insertion | In_Frame_Ins | novel | c.765_766insACA | p.Ala255_His256insThr | p.A255_H256insT | Q2NL82 | protein_coding | TCGA-BH-A0HB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | ||
| TSR1 | SNV | Missense_Mutation | c.1279G>A | p.Glu427Lys | p.E427K | Q2NL82 | protein_coding | tolerated(0.34) | benign(0.156) | TCGA-DG-A2KM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| TSR1 | SNV | Missense_Mutation | c.2395N>T | p.Pro799Ser | p.P799S | Q2NL82 | protein_coding | tolerated_low_confidence(0.22) | benign(0) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| TSR1 | SNV | Missense_Mutation | rs748274796 | c.972N>A | p.Met324Ile | p.M324I | Q2NL82 | protein_coding | deleterious(0.03) | benign(0.007) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 |
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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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