|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: TSC2 |
Gene summary for TSC2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TSC2 | Gene ID | 7249 |
| Gene name | TSC complex subunit 2 | |
| Gene Alias | LAM | |
| Cytomap | 16p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000422 | UniProtAcc | P49815 |
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 |
| 7249 | TSC2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.22e-04 | 3.89e-01 | -0.1808 |
| 7249 | TSC2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.15e-02 | 5.45e-01 | 0.0216 |
| 7249 | TSC2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.78e-08 | 5.31e-01 | -0.0811 |
| 7249 | TSC2 | HTA11_78_2000001011 | Human | Colorectum | AD | 4.27e-02 | 2.95e-01 | -0.1088 |
| 7249 | TSC2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.47e-14 | 4.67e-01 | -0.1954 |
| 7249 | TSC2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 6.02e-07 | 4.47e-01 | -0.1207 |
| 7249 | TSC2 | HTA11_83_2000001011 | Human | Colorectum | SER | 7.62e-04 | 4.44e-01 | -0.1526 |
| 7249 | TSC2 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.16e-16 | 5.84e-01 | -0.1464 |
| 7249 | TSC2 | HTA11_866_2000001011 | Human | Colorectum | AD | 6.11e-08 | 4.20e-01 | -0.1001 |
| 7249 | TSC2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.94e-04 | 3.36e-01 | -0.059 |
| 7249 | TSC2 | HTA11_546_2000001011 | Human | Colorectum | AD | 8.29e-05 | 4.50e-01 | -0.0842 |
| 7249 | TSC2 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.09e-08 | 4.20e-01 | 0.096 |
| 7249 | TSC2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 6.30e-08 | 5.13e-01 | 0.0338 |
| 7249 | TSC2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.92e-12 | 4.93e-01 | 0.0674 |
| 7249 | TSC2 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.53e-02 | 4.43e-01 | 0.0112 |
| 7249 | TSC2 | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.06e-02 | 3.43e-01 | 0.0588 |
| 7249 | TSC2 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 2.84e-03 | 9.05e-01 | 0.3487 |
| 7249 | TSC2 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.15e-04 | 3.48e-01 | 0.281 |
| 7249 | TSC2 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.86e-06 | 4.01e-01 | 0.3859 |
| 7249 | TSC2 | A015-C-104 | Human | Colorectum | FAP | 3.31e-03 | 1.12e-01 | -0.1899 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| 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:000268311 | Breast | IDC | negative regulation of immune system process | 55/1434 | 434/18723 | 1.53e-04 | 2.67e-03 | 55 |
| GO:004887214 | Breast | IDC | homeostasis of number of cells | 36/1434 | 272/18723 | 9.10e-04 | 1.04e-02 | 36 |
| GO:0070229 | Breast | IDC | negative regulation of lymphocyte apoptotic process | 7/1434 | 30/18723 | 6.48e-03 | 4.56e-02 | 7 |
| GO:000268321 | Breast | DCIS | negative regulation of immune system process | 57/1390 | 434/18723 | 1.81e-05 | 4.35e-04 | 57 |
| GO:004887224 | Breast | DCIS | homeostasis of number of cells | 36/1390 | 272/18723 | 5.17e-04 | 6.73e-03 | 36 |
| GO:0009896 | Colorectum | AD | positive regulation of catabolic process | 180/3918 | 492/18723 | 4.33e-16 | 1.94e-13 | 180 |
| GO:0031331 | Colorectum | AD | positive regulation of cellular catabolic process | 156/3918 | 427/18723 | 4.68e-14 | 1.05e-11 | 156 |
| GO:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0072594 | Colorectum | AD | establishment of protein localization to organelle | 148/3918 | 422/18723 | 7.95e-12 | 1.04e-09 | 148 |
| GO:0022411 | Colorectum | AD | cellular component disassembly | 147/3918 | 443/18723 | 8.53e-10 | 6.76e-08 | 147 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0006913 | Colorectum | AD | nucleocytoplasmic transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0051169 | Colorectum | AD | nuclear transport | 102/3918 | 301/18723 | 1.00e-07 | 4.85e-06 | 102 |
| GO:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0032868 | Colorectum | AD | response to insulin | 91/3918 | 264/18723 | 2.02e-07 | 8.48e-06 | 91 |
| GO:0010821 | Colorectum | AD | regulation of mitochondrion organization | 57/3918 | 144/18723 | 2.43e-07 | 9.92e-06 | 57 |
| GO:1901653 | Colorectum | AD | cellular response to peptide | 114/3918 | 359/18723 | 8.32e-07 | 2.88e-05 | 114 |
| GO:0032869 | Colorectum | AD | cellular response to insulin stimulus | 72/3918 | 203/18723 | 1.10e-06 | 3.68e-05 | 72 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04714210 | Oral cavity | LP | Thermogenesis | 105/2418 | 232/8465 | 3.14e-08 | 4.98e-07 | 3.21e-07 | 105 |
| hsa0421827 | Oral cavity | LP | Cellular senescence | 71/2418 | 156/8465 | 4.17e-06 | 3.75e-05 | 2.42e-05 | 71 |
| hsa0411523 | Oral cavity | LP | p53 signaling pathway | 38/2418 | 74/8465 | 2.82e-05 | 1.92e-04 | 1.24e-04 | 38 |
| hsa0516523 | Oral cavity | LP | Human papillomavirus infection | 121/2418 | 331/8465 | 8.00e-04 | 3.86e-03 | 2.49e-03 | 121 |
| hsa0516329 | Oral cavity | LP | Human cytomegalovirus infection | 85/2418 | 225/8465 | 1.55e-03 | 6.89e-03 | 4.45e-03 | 85 |
| hsa0414024 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
| hsa0471438 | Oral cavity | LP | Thermogenesis | 105/2418 | 232/8465 | 3.14e-08 | 4.98e-07 | 3.21e-07 | 105 |
| hsa0421837 | Oral cavity | LP | Cellular senescence | 71/2418 | 156/8465 | 4.17e-06 | 3.75e-05 | 2.42e-05 | 71 |
| hsa0411533 | Oral cavity | LP | p53 signaling pathway | 38/2418 | 74/8465 | 2.82e-05 | 1.92e-04 | 1.24e-04 | 38 |
| hsa0516533 | Oral cavity | LP | Human papillomavirus infection | 121/2418 | 331/8465 | 8.00e-04 | 3.86e-03 | 2.49e-03 | 121 |
| hsa0516337 | Oral cavity | LP | Human cytomegalovirus infection | 85/2418 | 225/8465 | 1.55e-03 | 6.89e-03 | 4.45e-03 | 85 |
| hsa0414034 | Oral cavity | LP | Autophagy - animal | 55/2418 | 141/8465 | 4.54e-03 | 1.87e-02 | 1.20e-02 | 55 |
| Page: 1 2 3 4 5 6 7 8 |
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 |
| TSC2 | SNV | Missense_Mutation | c.2106N>A | p.Asp702Glu | p.D702E | P49815 | protein_coding | deleterious(0.01) | probably_damaging(0.992) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| TSC2 | SNV | Missense_Mutation | c.4571N>T | p.Ser1524Leu | p.S1524L | P49815 | protein_coding | tolerated(0.14) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TSC2 | SNV | Missense_Mutation | c.2828N>A | p.Arg943Lys | p.R943K | P49815 | protein_coding | tolerated(0.09) | possibly_damaging(0.867) | TCGA-AC-A2B8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | chemo | PD | |
| TSC2 | SNV | Missense_Mutation | c.4346C>G | p.Ser1449Cys | p.S1449C | P49815 | protein_coding | tolerated(0.12) | probably_damaging(0.987) | TCGA-B6-A0RQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TSC2 | SNV | Missense_Mutation | c.1702N>G | p.Leu568Val | p.L568V | P49815 | protein_coding | tolerated(0.17) | probably_damaging(0.987) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | |
| TSC2 | SNV | Missense_Mutation | c.1273N>T | p.Asn425Tyr | p.N425Y | P49815 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-D8-A147-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine | SD | |
| TSC2 | SNV | Missense_Mutation | c.539N>C | p.Leu180Pro | p.L180P | P49815 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-E9-A1RB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | methotrexate | SD | |
| TSC2 | insertion | Frame_Shift_Ins | novel | c.2666_2667insATTGAAGAAATTAGACAAATTCAGGGAA | p.His890LeufsTer34 | p.H890Lfs*34 | P49815 | protein_coding | TCGA-B6-A0I5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TSC2 | deletion | Frame_Shift_Del | novel | c.3113delT | p.Phe1038SerfsTer15 | p.F1038Sfs*15 | P49815 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TSC2 | SNV | Missense_Mutation | rs764925296 | c.629C>T | p.Ala210Val | p.A210V | P49815 | protein_coding | tolerated(0.46) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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 |
| 7249 | TSC2 | CLINICALLY ACTIONABLE, KINASE, TUMOR SUPPRESSOR | EVEROLIMUS | EVEROLIMUS | 23158522,25295501 | |
| 7249 | TSC2 | CLINICALLY ACTIONABLE, KINASE, TUMOR SUPPRESSOR | Everolimus | EVEROLIMUS | ||
| 7249 | TSC2 | CLINICALLY ACTIONABLE, KINASE, TUMOR SUPPRESSOR | MTOR INHIBITOR | 26831717 |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |