|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TSR2 |
Gene summary for TSR2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TSR2 | Gene ID | 90121 |
| Gene name | TSR2 ribosome maturation factor | |
| Gene Alias | DBA14 | |
| Cytomap | Xp11.22 | |
| Gene Type | protein-coding | GO ID | GO:0000462 | UniProtAcc | A0A024R9U9 |
Top |
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 |
| 90121 | TSR2 | P40T-E | Human | Esophagus | ESCC | 4.60e-09 | 3.28e-01 | 0.109 |
| 90121 | TSR2 | P42T-E | Human | Esophagus | ESCC | 2.53e-15 | 4.26e-01 | 0.1175 |
| 90121 | TSR2 | P44T-E | Human | Esophagus | ESCC | 5.56e-15 | 3.56e-01 | 0.1096 |
| 90121 | TSR2 | P47T-E | Human | Esophagus | ESCC | 2.96e-29 | 5.88e-01 | 0.1067 |
| 90121 | TSR2 | P48T-E | Human | Esophagus | ESCC | 1.14e-14 | 3.21e-01 | 0.0959 |
| 90121 | TSR2 | P49T-E | Human | Esophagus | ESCC | 3.72e-09 | 9.90e-01 | 0.1768 |
| 90121 | TSR2 | P52T-E | Human | Esophagus | ESCC | 1.55e-36 | 7.38e-01 | 0.1555 |
| 90121 | TSR2 | P54T-E | Human | Esophagus | ESCC | 2.39e-20 | 5.03e-01 | 0.0975 |
| 90121 | TSR2 | P56T-E | Human | Esophagus | ESCC | 1.19e-15 | 1.31e+00 | 0.1613 |
| 90121 | TSR2 | P57T-E | Human | Esophagus | ESCC | 2.56e-26 | 4.26e-01 | 0.0926 |
| 90121 | TSR2 | P61T-E | Human | Esophagus | ESCC | 1.93e-25 | 7.98e-01 | 0.099 |
| 90121 | TSR2 | P62T-E | Human | Esophagus | ESCC | 5.93e-34 | 7.08e-01 | 0.1302 |
| 90121 | TSR2 | P65T-E | Human | Esophagus | ESCC | 1.61e-21 | 3.87e-01 | 0.0978 |
| 90121 | TSR2 | P74T-E | Human | Esophagus | ESCC | 6.20e-26 | 8.79e-01 | 0.1479 |
| 90121 | TSR2 | P75T-E | Human | Esophagus | ESCC | 9.05e-41 | 7.80e-01 | 0.1125 |
| 90121 | TSR2 | P76T-E | Human | Esophagus | ESCC | 1.80e-34 | 6.03e-01 | 0.1207 |
| 90121 | TSR2 | P79T-E | Human | Esophagus | ESCC | 9.53e-77 | 1.54e+00 | 0.1154 |
| 90121 | TSR2 | P80T-E | Human | Esophagus | ESCC | 2.53e-43 | 1.18e+00 | 0.155 |
| 90121 | TSR2 | P82T-E | Human | Esophagus | ESCC | 1.93e-17 | 8.39e-01 | 0.1072 |
| 90121 | TSR2 | P83T-E | Human | Esophagus | ESCC | 1.17e-26 | 7.27e-01 | 0.1738 |
| 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. |
Top |
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:002261327 | Esophagus | HGIN | ribonucleoprotein complex biogenesis | 158/2587 | 463/18723 | 2.61e-29 | 5.23e-26 | 158 |
| GO:004225426 | Esophagus | HGIN | ribosome biogenesis | 101/2587 | 299/18723 | 8.74e-19 | 4.03e-16 | 101 |
| GO:001607219 | Esophagus | HGIN | rRNA metabolic process | 72/2587 | 236/18723 | 2.26e-11 | 2.56e-09 | 72 |
| GO:000636419 | Esophagus | HGIN | rRNA processing | 69/2587 | 225/18723 | 4.53e-11 | 5.04e-09 | 69 |
| GO:003447010 | Esophagus | HGIN | ncRNA processing | 97/2587 | 395/18723 | 5.92e-09 | 3.90e-07 | 97 |
| GO:004227427 | Esophagus | HGIN | ribosomal small subunit biogenesis | 27/2587 | 73/18723 | 6.26e-07 | 2.72e-05 | 27 |
| GO:00346606 | Esophagus | HGIN | ncRNA metabolic process | 104/2587 | 485/18723 | 2.26e-06 | 8.23e-05 | 104 |
| 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:00304904 | Esophagus | ESCC | maturation of SSU-rRNA | 45/8552 | 50/18723 | 5.07e-11 | 1.63e-09 | 45 |
| 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:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
| GO:004225412 | Liver | Cirrhotic | ribosome biogenesis | 154/4634 | 299/18723 | 1.18e-23 | 6.72e-21 | 154 |
| GO:000636412 | Liver | Cirrhotic | rRNA processing | 115/4634 | 225/18723 | 1.12e-17 | 1.64e-15 | 115 |
| GO:00160724 | Liver | Cirrhotic | rRNA metabolic process | 119/4634 | 236/18723 | 1.19e-17 | 1.70e-15 | 119 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
Top |
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 |
Top |
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 |
Top |
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 |
| TSR2 | SNV | Missense_Mutation | c.349N>G | p.Gln117Glu | p.Q117E | Q969E8 | protein_coding | deleterious(0.03) | possibly_damaging(0.446) | TCGA-AR-A1AN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | |
| TSR2 | SNV | Missense_Mutation | c.167G>A | p.Arg56His | p.R56H | Q969E8 | protein_coding | tolerated(0.19) | possibly_damaging(0.52) | TCGA-E9-A22E-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphane | SD | |
| TSR2 | SNV | Missense_Mutation | novel | c.370N>T | p.Ala124Ser | p.A124S | Q969E8 | protein_coding | deleterious(0.05) | possibly_damaging(0.723) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TSR2 | SNV | Missense_Mutation | novel | c.345N>G | p.Ile115Met | p.I115M | Q969E8 | protein_coding | deleterious(0.05) | benign(0.145) | TCGA-MY-A5BF-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | CR |
| TSR2 | SNV | Missense_Mutation | novel | c.112N>T | p.His38Tyr | p.H38Y | Q969E8 | protein_coding | tolerated(0.54) | benign(0.006) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| TSR2 | SNV | Missense_Mutation | rs374472583 | c.166N>T | p.Arg56Cys | p.R56C | Q969E8 | protein_coding | tolerated(0.1) | possibly_damaging(0.593) | TCGA-G4-6304-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Chemotherapy | fluorouracil | PD |
| TSR2 | SNV | Missense_Mutation | novel | c.544N>T | p.Asp182Tyr | p.D182Y | Q969E8 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TSR2 | SNV | Missense_Mutation | novel | c.93N>T | p.Glu31Asp | p.E31D | Q969E8 | protein_coding | tolerated(0.36) | benign(0.085) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TSR2 | SNV | Missense_Mutation | novel | c.93N>T | p.Glu31Asp | p.E31D | Q969E8 | protein_coding | tolerated(0.36) | benign(0.085) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TSR2 | SNV | Missense_Mutation | novel | c.566N>T | p.Arg189Ile | p.R189I | Q969E8 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 |
Top |
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 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |