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Gene: TBC1D2B |
Gene summary for TBC1D2B |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TBC1D2B | Gene ID | 23102 |
| Gene name | TBC1 domain family member 2B | |
| Gene Alias | NEDSGO | |
| Cytomap | 15q24.3-q25.1 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9UPU7 |
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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 |
| 23102 | TBC1D2B | NAFLD1 | Human | Liver | NAFLD | 8.72e-08 | 8.53e-01 | -0.04 |
| 23102 | TBC1D2B | S41 | Human | Liver | Cirrhotic | 8.58e-04 | 5.05e-01 | -0.0343 |
| 23102 | TBC1D2B | HCC1_Meng | Human | Liver | HCC | 2.42e-13 | -1.04e-01 | 0.0246 |
| 23102 | TBC1D2B | HCC2_Meng | Human | Liver | HCC | 1.92e-07 | -3.29e-02 | 0.0107 |
| 23102 | TBC1D2B | male-WTA | Human | Thyroid | PTC | 2.93e-09 | 1.06e-01 | 0.1037 |
| 23102 | TBC1D2B | PTC04 | Human | Thyroid | PTC | 1.64e-13 | 1.45e-01 | 0.1927 |
| 23102 | TBC1D2B | PTC05 | Human | Thyroid | PTC | 3.84e-06 | 2.32e-01 | 0.2065 |
| 23102 | TBC1D2B | PTC06 | Human | Thyroid | PTC | 2.02e-12 | 2.53e-01 | 0.2057 |
| 23102 | TBC1D2B | PTC07 | Human | Thyroid | PTC | 9.40e-14 | 1.96e-01 | 0.2044 |
| 23102 | TBC1D2B | ATC09 | Human | Thyroid | ATC | 6.14e-04 | 1.97e-01 | 0.2871 |
| 23102 | TBC1D2B | ATC11 | Human | Thyroid | ATC | 5.55e-07 | 4.93e-01 | 0.3386 |
| 23102 | TBC1D2B | ATC12 | Human | Thyroid | ATC | 2.71e-17 | 3.37e-01 | 0.34 |
| 23102 | TBC1D2B | ATC13 | Human | Thyroid | ATC | 9.86e-24 | 4.10e-01 | 0.34 |
| 23102 | TBC1D2B | ATC1 | Human | Thyroid | ATC | 1.03e-04 | 2.36e-01 | 0.2878 |
| 23102 | TBC1D2B | ATC2 | Human | Thyroid | ATC | 6.06e-08 | 1.02e+00 | 0.34 |
| 23102 | TBC1D2B | ATC3 | Human | Thyroid | ATC | 3.50e-13 | 6.66e-01 | 0.338 |
| 23102 | TBC1D2B | ATC4 | Human | Thyroid | ATC | 1.80e-19 | 4.25e-01 | 0.34 |
| 23102 | TBC1D2B | ATC5 | Human | Thyroid | ATC | 6.75e-30 | 4.50e-01 | 0.34 |
| Page: 1 |
| 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 |
| Esophagus | ESCC |  |
| Skin | AK |  |
| Skin | SCCIS |  |
| Skin | cSCC |  |
| Thyroid | HT |  |
| ∗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:00430875 | Liver | NAFLD | regulation of GTPase activity | 62/1882 | 348/18723 | 5.65e-06 | 2.03e-04 | 62 |
| GO:00435474 | Liver | NAFLD | positive regulation of GTPase activity | 45/1882 | 255/18723 | 1.30e-04 | 2.47e-03 | 45 |
| GO:00906301 | Liver | NAFLD | activation of GTPase activity | 22/1882 | 115/18723 | 2.28e-03 | 2.19e-02 | 22 |
| GO:004308718 | Thyroid | PTC | regulation of GTPase activity | 148/5968 | 348/18723 | 1.63e-05 | 1.71e-04 | 148 |
| GO:004354714 | Thyroid | PTC | positive regulation of GTPase activity | 103/5968 | 255/18723 | 2.38e-03 | 1.25e-02 | 103 |
| GO:004308719 | Thyroid | ATC | regulation of GTPase activity | 153/6293 | 348/18723 | 3.24e-05 | 2.68e-04 | 153 |
| GO:004354715 | Thyroid | ATC | positive regulation of GTPase activity | 106/6293 | 255/18723 | 4.58e-03 | 1.89e-02 | 106 |
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| 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 |
| TBC1D2B | SNV | Missense_Mutation | c.2777A>G | p.Glu926Gly | p.E926G | Q9UPU7 | protein_coding | deleterious(0) | probably_damaging(0.951) | TCGA-AO-A0J4-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TBC1D2B | SNV | Missense_Mutation | c.1118N>A | p.Arg373Gln | p.R373Q | Q9UPU7 | protein_coding | deleterious(0.02) | probably_damaging(0.944) | TCGA-B6-A0IE-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| TBC1D2B | SNV | Missense_Mutation | c.2147N>C | p.Arg716Pro | p.R716P | Q9UPU7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A0DO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TBC1D2B | SNV | Missense_Mutation | novel | c.619N>A | p.Pro207Thr | p.P207T | Q9UPU7 | protein_coding | deleterious(0.04) | possibly_damaging(0.663) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| TBC1D2B | SNV | Missense_Mutation | c.2062N>A | p.Glu688Lys | p.E688K | Q9UPU7 | protein_coding | tolerated(0.59) | benign(0.001) | TCGA-E2-A1IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
| TBC1D2B | SNV | Missense_Mutation | novel | c.808C>A | p.Gln270Lys | p.Q270K | Q9UPU7 | protein_coding | tolerated(0.69) | benign(0.023) | TCGA-E2-A1LS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cyclophosphamide | SD |
| TBC1D2B | SNV | Missense_Mutation | novel | c.1855N>T | p.Asp619Tyr | p.D619Y | Q9UPU7 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-HN-A2NL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| TBC1D2B | insertion | In_Frame_Ins | novel | c.1816_1817insCCCAACAAC | p.Asp606delinsAlaGlnGlnHis | p.D606delinsAQQH | Q9UPU7 | protein_coding | TCGA-A8-A09T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| TBC1D2B | insertion | Nonsense_Mutation | novel | c.1815_1816insTGAGCTGGACTTGCTGCGAACTCT | p.Asp605_Asp606insTer | p.D605_D606ins* | Q9UPU7 | protein_coding | TCGA-A8-A09T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | ||
| TBC1D2B | insertion | Frame_Shift_Ins | novel | c.1930_1931insTC | p.Thr644IlefsTer3 | p.T644Ifs*3 | Q9UPU7 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | 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 |
| Page: 1 |
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