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Gene: TBC1D4 |
Gene summary for TBC1D4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TBC1D4 | Gene ID | 9882 |
| Gene name | TBC1 domain family member 4 | |
| Gene Alias | AS160 | |
| Cytomap | 13q22.2 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | O60343 |
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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 |
| 9882 | TBC1D4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.24e-11 | -5.70e-01 | 0.0155 |
| 9882 | TBC1D4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.57e-03 | -5.19e-01 | -0.1808 |
| 9882 | TBC1D4 | HTA11_2951_2000001011 | Human | Colorectum | AD | 4.40e-05 | -8.35e-01 | 0.0216 |
| 9882 | TBC1D4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 7.92e-04 | -5.89e-01 | -0.1207 |
| 9882 | TBC1D4 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.43e-07 | -3.90e-01 | -0.1464 |
| 9882 | TBC1D4 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.23e-06 | -4.09e-01 | -0.1001 |
| 9882 | TBC1D4 | HTA11_8622_2000001021 | Human | Colorectum | SER | 6.42e-03 | -6.51e-01 | 0.0528 |
| 9882 | TBC1D4 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.54e-04 | -5.23e-01 | 0.0338 |
| 9882 | TBC1D4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.27e-02 | -3.37e-01 | 0.0674 |
| 9882 | TBC1D4 | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.06e-03 | -5.69e-01 | 0.0588 |
| 9882 | TBC1D4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.62e-03 | -2.26e-01 | 0.294 |
| 9882 | TBC1D4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 3.11e-08 | 6.90e-01 | 0.281 |
| 9882 | TBC1D4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.59e-13 | -4.84e-01 | 0.3005 |
| 9882 | TBC1D4 | A002-C-010 | Human | Colorectum | FAP | 2.42e-05 | -1.91e-01 | 0.242 |
| 9882 | TBC1D4 | A001-C-207 | Human | Colorectum | FAP | 9.09e-03 | -2.85e-01 | 0.1278 |
| 9882 | TBC1D4 | A015-C-203 | Human | Colorectum | FAP | 2.03e-24 | -3.07e-01 | -0.1294 |
| 9882 | TBC1D4 | A015-C-204 | Human | Colorectum | FAP | 9.43e-05 | -3.17e-01 | -0.0228 |
| 9882 | TBC1D4 | A014-C-040 | Human | Colorectum | FAP | 4.83e-03 | -4.04e-01 | -0.1184 |
| 9882 | TBC1D4 | A002-C-201 | Human | Colorectum | FAP | 3.17e-14 | -4.93e-01 | 0.0324 |
| 9882 | TBC1D4 | A002-C-203 | Human | Colorectum | FAP | 6.73e-07 | -2.94e-01 | 0.2786 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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:001063913 | Lung | AIS | negative regulation of organelle organization | 61/1849 | 348/18723 | 6.53e-06 | 2.92e-04 | 61 |
| GO:004354711 | Lung | AIS | positive regulation of GTPase activity | 44/1849 | 255/18723 | 1.74e-04 | 3.64e-03 | 44 |
| GO:009063011 | Lung | AIS | activation of GTPase activity | 21/1849 | 115/18723 | 4.07e-03 | 3.65e-02 | 21 |
| GO:190165324 | Thyroid | HT | cellular response to peptide | 46/1272 | 359/18723 | 2.46e-05 | 5.48e-04 | 46 |
| GO:004343427 | Thyroid | HT | response to peptide hormone | 49/1272 | 414/18723 | 1.05e-04 | 1.75e-03 | 49 |
| GO:001063925 | Thyroid | HT | negative regulation of organelle organization | 39/1272 | 348/18723 | 1.45e-03 | 1.36e-02 | 39 |
| GO:007137519 | Thyroid | HT | cellular response to peptide hormone stimulus | 33/1272 | 290/18723 | 2.53e-03 | 2.12e-02 | 33 |
| GO:001605016 | Thyroid | HT | vesicle organization | 33/1272 | 300/18723 | 4.30e-03 | 3.13e-02 | 33 |
| GO:003286920 | Thyroid | HT | cellular response to insulin stimulus | 24/1272 | 203/18723 | 5.72e-03 | 3.72e-02 | 24 |
| GO:003286820 | Thyroid | HT | response to insulin | 29/1272 | 264/18723 | 7.25e-03 | 4.35e-02 | 29 |
| GO:001605017 | Thyroid | PTC | vesicle organization | 163/5968 | 300/18723 | 4.74e-16 | 3.69e-14 | 163 |
| GO:1901653111 | Thyroid | PTC | cellular response to peptide | 169/5968 | 359/18723 | 9.81e-10 | 2.89e-08 | 169 |
| GO:0010639112 | Thyroid | PTC | negative regulation of organelle organization | 163/5968 | 348/18723 | 3.04e-09 | 8.39e-08 | 163 |
| GO:0043434113 | Thyroid | PTC | response to peptide hormone | 188/5968 | 414/18723 | 4.13e-09 | 1.09e-07 | 188 |
| GO:0071375110 | Thyroid | PTC | cellular response to peptide hormone stimulus | 136/5968 | 290/18723 | 5.49e-08 | 1.17e-06 | 136 |
| GO:0032869111 | Thyroid | PTC | cellular response to insulin stimulus | 100/5968 | 203/18723 | 1.70e-07 | 3.19e-06 | 100 |
| GO:0032868111 | Thyroid | PTC | response to insulin | 124/5968 | 264/18723 | 1.87e-07 | 3.47e-06 | 124 |
| GO:00482846 | Thyroid | PTC | organelle fusion | 71/5968 | 141/18723 | 3.68e-06 | 4.70e-05 | 71 |
| GO:004308718 | Thyroid | PTC | regulation of GTPase activity | 148/5968 | 348/18723 | 1.63e-05 | 1.71e-04 | 148 |
| GO:00610256 | Thyroid | PTC | membrane fusion | 77/5968 | 163/18723 | 2.86e-05 | 2.78e-04 | 77 |
| Page: 1 2 3 4 5 6 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
| hsa04919 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
| hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
| hsa049191 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
| hsa054152 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
| hsa049192 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
| hsa054153 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
| hsa049193 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
| hsa054154 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
| hsa049194 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
| hsa04931 | Colorectum | MSS | Insulin resistance | 36/1875 | 108/8465 | 4.74e-03 | 2.01e-02 | 1.23e-02 | 36 |
| hsa054155 | Colorectum | MSS | Diabetic cardiomyopathy | 106/1875 | 203/8465 | 2.47e-21 | 1.62e-19 | 9.92e-20 | 106 |
| hsa049195 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
| hsa049311 | Colorectum | MSS | Insulin resistance | 36/1875 | 108/8465 | 4.74e-03 | 2.01e-02 | 1.23e-02 | 36 |
| hsa054158 | Colorectum | FAP | Diabetic cardiomyopathy | 70/1404 | 203/8465 | 2.62e-10 | 2.18e-08 | 1.33e-08 | 70 |
| hsa049198 | Colorectum | FAP | Thyroid hormone signaling pathway | 41/1404 | 121/8465 | 2.28e-06 | 4.28e-05 | 2.60e-05 | 41 |
| hsa049312 | Colorectum | FAP | Insulin resistance | 32/1404 | 108/8465 | 4.90e-04 | 3.56e-03 | 2.16e-03 | 32 |
| hsa054159 | Colorectum | FAP | Diabetic cardiomyopathy | 70/1404 | 203/8465 | 2.62e-10 | 2.18e-08 | 1.33e-08 | 70 |
| hsa049199 | Colorectum | FAP | Thyroid hormone signaling pathway | 41/1404 | 121/8465 | 2.28e-06 | 4.28e-05 | 2.60e-05 | 41 |
| hsa049313 | Colorectum | FAP | Insulin resistance | 32/1404 | 108/8465 | 4.90e-04 | 3.56e-03 | 2.16e-03 | 32 |
| Page: 1 2 |
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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 |
| TBC1D4 | SNV | Missense_Mutation | c.782G>A | p.Gly261Glu | p.G261E | O60343 | protein_coding | tolerated(0.19) | benign(0.021) | TCGA-A2-A25B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | PD | |
| TBC1D4 | SNV | Missense_Mutation | c.1826C>T | p.Ser609Phe | p.S609F | O60343 | protein_coding | deleterious(0.01) | benign(0.02) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR | |
| TBC1D4 | SNV | Missense_Mutation | c.1153A>T | p.Ile385Phe | p.I385F | O60343 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TBC1D4 | SNV | Missense_Mutation | c.208N>A | p.Glu70Lys | p.E70K | O60343 | protein_coding | tolerated(0.68) | benign(0.078) | TCGA-AN-A0XO-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TBC1D4 | SNV | Missense_Mutation | novel | c.1715N>G | p.Glu572Gly | p.E572G | O60343 | protein_coding | deleterious(0) | possibly_damaging(0.701) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| TBC1D4 | SNV | Missense_Mutation | c.2619N>C | p.Arg873Ser | p.R873S | O60343 | protein_coding | tolerated(0.07) | probably_damaging(0.954) | TCGA-B6-A1KN-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
| TBC1D4 | SNV | Missense_Mutation | c.1370N>G | p.Pro457Arg | p.P457R | O60343 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TBC1D4 | SNV | Missense_Mutation | c.3340G>A | p.Glu1114Lys | p.E1114K | O60343 | protein_coding | deleterious(0) | benign(0.297) | TCGA-BH-A18P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| TBC1D4 | SNV | Missense_Mutation | c.3589G>A | p.Glu1197Lys | p.E1197K | O60343 | protein_coding | deleterious(0.01) | possibly_damaging(0.725) | TCGA-C8-A12T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TBC1D4 | SNV | Missense_Mutation | rs370555579 | c.982G>A | p.Glu328Lys | p.E328K | O60343 | protein_coding | tolerated(0.13) | benign(0.419) | TCGA-C8-A130-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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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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