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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 | HCC2_Meng | Human | Liver | HCC | 6.20e-12 | 4.99e-02 | 0.0107 |
| 55720 | TSR1 | HCC1 | Human | Liver | HCC | 2.29e-02 | 2.92e+00 | 0.5336 |
| 55720 | TSR1 | HCC2 | Human | Liver | HCC | 2.01e-08 | 3.67e+00 | 0.5341 |
| 55720 | TSR1 | S014 | Human | Liver | HCC | 8.11e-11 | 4.73e-01 | 0.2254 |
| 55720 | TSR1 | S015 | Human | Liver | HCC | 3.21e-06 | 4.11e-01 | 0.2375 |
| 55720 | TSR1 | S016 | Human | Liver | HCC | 1.21e-17 | 6.24e-01 | 0.2243 |
| 55720 | TSR1 | S027 | Human | Liver | HCC | 4.23e-05 | 5.94e-01 | 0.2446 |
| 55720 | TSR1 | S028 | Human | Liver | HCC | 1.44e-09 | 6.41e-01 | 0.2503 |
| 55720 | TSR1 | S029 | Human | Liver | HCC | 2.97e-14 | 6.67e-01 | 0.2581 |
| 55720 | TSR1 | C04 | Human | Oral cavity | OSCC | 6.90e-18 | 8.39e-01 | 0.2633 |
| 55720 | TSR1 | C21 | Human | Oral cavity | OSCC | 2.50e-30 | 9.64e-01 | 0.2678 |
| 55720 | TSR1 | C30 | Human | Oral cavity | OSCC | 6.34e-29 | 1.57e+00 | 0.3055 |
| 55720 | TSR1 | C43 | Human | Oral cavity | OSCC | 2.74e-11 | 3.42e-01 | 0.1704 |
| 55720 | TSR1 | C46 | Human | Oral cavity | OSCC | 1.25e-05 | 1.49e-01 | 0.1673 |
| 55720 | TSR1 | C51 | Human | Oral cavity | OSCC | 3.52e-09 | 6.50e-01 | 0.2674 |
| 55720 | TSR1 | C07 | Human | Oral cavity | OSCC | 3.78e-02 | 5.21e-01 | 0.2491 |
| 55720 | TSR1 | C08 | Human | Oral cavity | OSCC | 4.26e-13 | 3.99e-01 | 0.1919 |
| 55720 | TSR1 | LN22 | Human | Oral cavity | OSCC | 1.22e-05 | 6.86e-01 | 0.1733 |
| 55720 | TSR1 | SYSMH1 | Human | Oral cavity | OSCC | 9.72e-08 | 2.42e-01 | 0.1127 |
| 55720 | TSR1 | SYSMH2 | Human | Oral cavity | OSCC | 9.87e-19 | 5.36e-01 | 0.2326 |
| 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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
| GO:0042254111 | Esophagus | ESCC | ribosome biogenesis | 252/8552 | 299/18723 | 3.27e-44 | 1.04e-40 | 252 |
| GO:003447015 | Esophagus | ESCC | ncRNA processing | 300/8552 | 395/18723 | 3.09e-35 | 3.26e-32 | 300 |
| GO:0016072110 | Esophagus | ESCC | rRNA metabolic process | 197/8552 | 236/18723 | 1.31e-33 | 1.18e-30 | 197 |
| GO:0006364110 | Esophagus | ESCC | rRNA processing | 189/8552 | 225/18723 | 4.88e-33 | 3.87e-30 | 189 |
| GO:003466012 | Esophagus | ESCC | ncRNA metabolic process | 346/8552 | 485/18723 | 4.35e-31 | 2.51e-28 | 346 |
| GO:0042274111 | Esophagus | ESCC | ribosomal small subunit biogenesis | 67/8552 | 73/18723 | 6.62e-17 | 5.38e-15 | 67 |
| GO:00905013 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:00304904 | Esophagus | ESCC | maturation of SSU-rRNA | 45/8552 | 50/18723 | 5.07e-11 | 1.63e-09 | 45 |
| GO:00903053 | Esophagus | ESCC | nucleic acid phosphodiester bond hydrolysis | 163/8552 | 261/18723 | 3.07e-08 | 5.73e-07 | 163 |
| GO:00004623 | Esophagus | ESCC | maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 32/8552 | 37/18723 | 2.96e-07 | 4.23e-06 | 32 |
| GO:00004693 | Esophagus | ESCC | cleavage involved in rRNA processing | 24/8552 | 27/18723 | 3.48e-06 | 3.84e-05 | 24 |
| GO:00905023 | Esophagus | ESCC | RNA phosphodiester bond hydrolysis, endonucleolytic | 55/8552 | 82/18723 | 7.34e-05 | 5.51e-04 | 55 |
| GO:00004783 | Esophagus | ESCC | endonucleolytic cleavage involved in rRNA processing | 14/8552 | 15/18723 | 1.47e-04 | 9.85e-04 | 14 |
| GO:00004793 | Esophagus | ESCC | endonucleolytic cleavage of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) | 14/8552 | 15/18723 | 1.47e-04 | 9.85e-04 | 14 |
| GO:002261322 | Liver | HCC | ribonucleoprotein complex biogenesis | 355/7958 | 463/18723 | 7.76e-52 | 4.92e-48 | 355 |
| GO:004225422 | Liver | HCC | ribosome biogenesis | 246/7958 | 299/18723 | 4.99e-46 | 1.58e-42 | 246 |
| GO:00344702 | Liver | HCC | ncRNA processing | 293/7958 | 395/18723 | 4.26e-38 | 6.76e-35 | 293 |
| GO:001607212 | Liver | HCC | rRNA metabolic process | 193/7958 | 236/18723 | 1.26e-35 | 1.14e-32 | 193 |
| GO:000636421 | Liver | HCC | rRNA processing | 185/7958 | 225/18723 | 8.14e-35 | 6.45e-32 | 185 |
| Page: 1 2 3 4 5 |
| 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 |
| 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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