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Gene: TBC1D1 |
Gene summary for TBC1D1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TBC1D1 | Gene ID | 23216 |
| Gene name | TBC1 domain family member 1 | |
| Gene Alias | TBC | |
| Cytomap | 4p14 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q86TI0 |
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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 |
| 23216 | TBC1D1 | S43 | Human | Liver | Cirrhotic | 1.12e-02 | 9.43e-03 | -0.0187 |
| 23216 | TBC1D1 | HCC1_Meng | Human | Liver | HCC | 4.23e-17 | -1.14e-01 | 0.0246 |
| 23216 | TBC1D1 | HCC2_Meng | Human | Liver | HCC | 1.24e-12 | -2.90e-02 | 0.0107 |
| 23216 | TBC1D1 | HCC1 | Human | Liver | HCC | 4.12e-02 | 3.46e+00 | 0.5336 |
| 23216 | TBC1D1 | HCC2 | Human | Liver | HCC | 1.66e-08 | 3.46e+00 | 0.5341 |
| 23216 | TBC1D1 | S014 | Human | Liver | HCC | 4.80e-04 | 3.53e-01 | 0.2254 |
| 23216 | TBC1D1 | S015 | Human | Liver | HCC | 2.57e-06 | 5.62e-01 | 0.2375 |
| 23216 | TBC1D1 | S016 | Human | Liver | HCC | 1.38e-07 | 4.83e-01 | 0.2243 |
| 23216 | TBC1D1 | S028 | Human | Liver | HCC | 1.41e-08 | 5.65e-01 | 0.2503 |
| 23216 | TBC1D1 | S029 | Human | Liver | HCC | 6.27e-12 | 6.12e-01 | 0.2581 |
| 23216 | TBC1D1 | male-WTA | Human | Thyroid | PTC | 8.76e-26 | 2.45e-01 | 0.1037 |
| 23216 | TBC1D1 | PTC01 | Human | Thyroid | PTC | 1.54e-15 | 1.13e-01 | 0.1899 |
| 23216 | TBC1D1 | PTC03 | Human | Thyroid | PTC | 4.74e-05 | 1.43e-01 | 0.1784 |
| 23216 | TBC1D1 | PTC04 | Human | Thyroid | PTC | 4.51e-11 | 2.22e-01 | 0.1927 |
| 23216 | TBC1D1 | PTC05 | Human | Thyroid | PTC | 2.91e-19 | 5.13e-01 | 0.2065 |
| 23216 | TBC1D1 | PTC06 | Human | Thyroid | PTC | 1.47e-26 | 3.79e-01 | 0.2057 |
| 23216 | TBC1D1 | PTC07 | Human | Thyroid | PTC | 1.14e-28 | 4.27e-01 | 0.2044 |
| 23216 | TBC1D1 | ATC09 | Human | Thyroid | ATC | 2.25e-07 | 7.43e-02 | 0.2871 |
| 23216 | TBC1D1 | ATC11 | Human | Thyroid | ATC | 3.36e-02 | 3.24e-01 | 0.3386 |
| 23216 | TBC1D1 | ATC12 | Human | Thyroid | ATC | 5.81e-05 | 1.07e-02 | 0.34 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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: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:0048193 | Colorectum | AD | Golgi vesicle transport | 109/3918 | 296/18723 | 1.80e-10 | 1.68e-08 | 109 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0010506 | Colorectum | AD | regulation of autophagy | 111/3918 | 317/18723 | 3.57e-09 | 2.35e-07 | 111 |
| GO:0016482 | Colorectum | AD | cytosolic transport | 68/3918 | 168/18723 | 6.00e-09 | 3.72e-07 | 68 |
| GO:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| GO:0043112 | Colorectum | AD | receptor metabolic process | 62/3918 | 166/18723 | 8.18e-07 | 2.85e-05 | 62 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0042147 | Colorectum | AD | retrograde transport, endosome to Golgi | 37/3918 | 91/18723 | 1.46e-05 | 3.14e-04 | 37 |
| GO:0001881 | Colorectum | AD | receptor recycling | 18/3918 | 33/18723 | 2.23e-05 | 4.40e-04 | 18 |
| GO:0010507 | Colorectum | AD | negative regulation of autophagy | 31/3918 | 85/18723 | 6.91e-04 | 7.05e-03 | 31 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:0001919 | Colorectum | AD | regulation of receptor recycling | 12/3918 | 23/18723 | 9.11e-04 | 8.71e-03 | 12 |
| GO:0007033 | Colorectum | AD | vacuole organization | 53/3918 | 180/18723 | 4.18e-03 | 2.89e-02 | 53 |
| GO:00313302 | Colorectum | MSS | negative regulation of cellular catabolic process | 96/3467 | 262/18723 | 2.67e-12 | 4.63e-10 | 96 |
| GO:00098952 | Colorectum | MSS | negative regulation of catabolic process | 110/3467 | 320/18723 | 7.88e-12 | 1.20e-09 | 110 |
| GO:00481932 | Colorectum | MSS | Golgi vesicle transport | 101/3467 | 296/18723 | 9.09e-11 | 9.77e-09 | 101 |
| GO:00161972 | Colorectum | MSS | endosomal transport | 79/3467 | 230/18723 | 7.04e-09 | 4.39e-07 | 79 |
| GO:00162362 | Colorectum | MSS | macroautophagy | 93/3467 | 291/18723 | 2.08e-08 | 1.17e-06 | 93 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0415221 | Liver | Cirrhotic | AMPK signaling pathway | 49/2530 | 121/8465 | 7.90e-03 | 2.74e-02 | 1.69e-02 | 49 |
| hsa0415231 | Liver | Cirrhotic | AMPK signaling pathway | 49/2530 | 121/8465 | 7.90e-03 | 2.74e-02 | 1.69e-02 | 49 |
| hsa0415241 | Liver | HCC | AMPK signaling pathway | 77/4020 | 121/8465 | 2.32e-04 | 1.11e-03 | 6.18e-04 | 77 |
| hsa0415251 | Liver | HCC | AMPK signaling pathway | 77/4020 | 121/8465 | 2.32e-04 | 1.11e-03 | 6.18e-04 | 77 |
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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 |
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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. |
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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 |
| TBC1D1 | SNV | Missense_Mutation | rs777583181 | c.3187G>A | p.Val1063Ile | p.V1063I | Q86TI0 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-A8-A08C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| TBC1D1 | SNV | Missense_Mutation | rs753335447 | c.46G>A | p.Glu16Lys | p.E16K | Q86TI0 | protein_coding | deleterious_low_confidence(0.05) | benign(0.014) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TBC1D1 | SNV | Missense_Mutation | c.3320N>A | p.Arg1107Lys | p.R1107K | Q86TI0 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| TBC1D1 | deletion | Frame_Shift_Del | rs760298745 | c.928delA | p.Ile310Ter | p.I310* | Q86TI0 | protein_coding | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| TBC1D1 | insertion | Frame_Shift_Ins | novel | c.1568_1569insGCCCT | p.His524ProfsTer17 | p.H524Pfs*17 | Q86TI0 | protein_coding | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TBC1D1 | insertion | In_Frame_Ins | novel | c.1569_1570insTATTCCTCTTCTAGT | p.Glu523_His524insTyrSerSerSerSer | p.E523_H524insYSSSS | Q86TI0 | protein_coding | TCGA-AN-A04C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| TBC1D1 | insertion | Frame_Shift_Ins | novel | c.2299_2300insAAAC | p.Leu767GlnfsTer3 | p.L767Qfs*3 | Q86TI0 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| TBC1D1 | insertion | Frame_Shift_Ins | novel | c.2757_2758insGTGACATTGTTTCTACATTTAAAAAATCTCTTTA | p.Met920ValfsTer38 | p.M920Vfs*38 | Q86TI0 | protein_coding | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| TBC1D1 | SNV | Missense_Mutation | rs540156102 | c.1418C>T | p.Ser473Leu | p.S473L | Q86TI0 | protein_coding | tolerated(0.28) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TBC1D1 | SNV | Missense_Mutation | rs765228485 | c.2896N>A | p.Ala966Thr | p.A966T | Q86TI0 | protein_coding | tolerated(0.08) | probably_damaging(1) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
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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 |
| 23216 | TBC1D1 | NA | olanzapine | OLANZAPINE | 23364847 | |
| 23216 | TBC1D1 | NA | clozapine | CLOZAPINE | 23364847 |
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