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Gene: TBC1D2 |
Gene summary for TBC1D2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TBC1D2 | Gene ID | 55357 |
| Gene name | TBC1 domain family member 2 | |
| Gene Alias | PARIS-1 | |
| Cytomap | 9q22.33 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | Q9BYX2 |
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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 |
| 55357 | TBC1D2 | P48T-E | Human | Esophagus | ESCC | 2.34e-28 | 5.34e-01 | 0.0959 |
| 55357 | TBC1D2 | P49T-E | Human | Esophagus | ESCC | 2.39e-06 | 6.62e-01 | 0.1768 |
| 55357 | TBC1D2 | P52T-E | Human | Esophagus | ESCC | 5.02e-22 | 5.32e-01 | 0.1555 |
| 55357 | TBC1D2 | P54T-E | Human | Esophagus | ESCC | 8.66e-30 | 6.62e-01 | 0.0975 |
| 55357 | TBC1D2 | P57T-E | Human | Esophagus | ESCC | 2.56e-09 | 2.39e-01 | 0.0926 |
| 55357 | TBC1D2 | P61T-E | Human | Esophagus | ESCC | 1.49e-10 | 3.19e-01 | 0.099 |
| 55357 | TBC1D2 | P62T-E | Human | Esophagus | ESCC | 6.07e-36 | 7.97e-01 | 0.1302 |
| 55357 | TBC1D2 | P65T-E | Human | Esophagus | ESCC | 5.85e-13 | 2.85e-01 | 0.0978 |
| 55357 | TBC1D2 | P74T-E | Human | Esophagus | ESCC | 9.01e-10 | 3.13e-01 | 0.1479 |
| 55357 | TBC1D2 | P75T-E | Human | Esophagus | ESCC | 3.75e-19 | 5.74e-01 | 0.1125 |
| 55357 | TBC1D2 | P76T-E | Human | Esophagus | ESCC | 1.20e-02 | 4.81e-02 | 0.1207 |
| 55357 | TBC1D2 | P79T-E | Human | Esophagus | ESCC | 2.00e-05 | 1.08e-01 | 0.1154 |
| 55357 | TBC1D2 | P80T-E | Human | Esophagus | ESCC | 2.75e-11 | 5.12e-01 | 0.155 |
| 55357 | TBC1D2 | P82T-E | Human | Esophagus | ESCC | 2.37e-09 | 4.72e-01 | 0.1072 |
| 55357 | TBC1D2 | P83T-E | Human | Esophagus | ESCC | 2.05e-37 | 8.67e-01 | 0.1738 |
| 55357 | TBC1D2 | P84T-E | Human | Esophagus | ESCC | 3.28e-13 | 6.48e-01 | 0.0933 |
| 55357 | TBC1D2 | P89T-E | Human | Esophagus | ESCC | 4.08e-07 | 4.39e-01 | 0.1752 |
| 55357 | TBC1D2 | P91T-E | Human | Esophagus | ESCC | 3.06e-06 | 7.60e-01 | 0.1828 |
| 55357 | TBC1D2 | P104T-E | Human | Esophagus | ESCC | 2.68e-02 | 1.01e-01 | 0.0931 |
| 55357 | TBC1D2 | P107T-E | Human | Esophagus | ESCC | 1.05e-30 | 8.81e-01 | 0.171 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| 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. |
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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:00430877 | Cervix | CC | regulation of GTPase activity | 79/2311 | 348/18723 | 4.21e-08 | 2.60e-06 | 79 |
| GO:00435476 | Cervix | CC | positive regulation of GTPase activity | 53/2311 | 255/18723 | 8.72e-05 | 1.16e-03 | 53 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:00430872 | Colorectum | MSS | regulation of GTPase activity | 101/3467 | 348/18723 | 1.00e-06 | 3.46e-05 | 101 |
| GO:00435471 | Colorectum | MSS | positive regulation of GTPase activity | 68/3467 | 255/18723 | 7.97e-04 | 8.38e-03 | 68 |
| GO:00430873 | Colorectum | FAP | regulation of GTPase activity | 85/2622 | 348/18723 | 1.20e-07 | 7.68e-06 | 85 |
| GO:00435472 | Colorectum | FAP | positive regulation of GTPase activity | 61/2622 | 255/18723 | 1.39e-05 | 3.73e-04 | 61 |
| GO:0090630 | Colorectum | FAP | activation of GTPase activity | 27/2622 | 115/18723 | 4.23e-03 | 2.90e-02 | 27 |
| GO:00430874 | Colorectum | CRC | regulation of GTPase activity | 69/2078 | 348/18723 | 1.11e-06 | 6.69e-05 | 69 |
| GO:00435473 | Colorectum | CRC | positive regulation of GTPase activity | 49/2078 | 255/18723 | 8.67e-05 | 1.77e-03 | 49 |
| GO:00430878 | Endometrium | AEH | regulation of GTPase activity | 66/2100 | 348/18723 | 1.26e-05 | 2.77e-04 | 66 |
| GO:00435477 | Endometrium | AEH | positive regulation of GTPase activity | 48/2100 | 255/18723 | 2.18e-04 | 2.67e-03 | 48 |
| GO:00906304 | Endometrium | AEH | activation of GTPase activity | 22/2100 | 115/18723 | 8.42e-03 | 4.60e-02 | 22 |
| GO:004308712 | Endometrium | EEC | regulation of GTPase activity | 67/2168 | 348/18723 | 1.84e-05 | 3.43e-04 | 67 |
| GO:004354712 | Endometrium | EEC | positive regulation of GTPase activity | 50/2168 | 255/18723 | 1.26e-04 | 1.66e-03 | 50 |
| GO:009063012 | Endometrium | EEC | activation of GTPase activity | 23/2168 | 115/18723 | 6.04e-03 | 3.57e-02 | 23 |
| GO:004819318 | Esophagus | ESCC | Golgi vesicle transport | 231/8552 | 296/18723 | 1.82e-30 | 9.63e-28 | 231 |
| GO:0016032111 | Esophagus | ESCC | viral process | 301/8552 | 415/18723 | 3.34e-29 | 1.32e-26 | 301 |
| GO:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| 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 |
| TBC1D2 | SNV | Missense_Mutation | rs534775698 | c.2122N>C | p.Thr708Pro | p.T708P | Q9BYX2 | protein_coding | tolerated(0.06) | possibly_damaging(0.522) | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD |
| TBC1D2 | SNV | Missense_Mutation | novel | c.2187G>T | p.Glu729Asp | p.E729D | Q9BYX2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TBC1D2 | SNV | Missense_Mutation | rs761820400 | c.1868G>A | p.Arg623Gln | p.R623Q | Q9BYX2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| TBC1D2 | SNV | Missense_Mutation | c.1691G>T | p.Gly564Val | p.G564V | Q9BYX2 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| TBC1D2 | SNV | Missense_Mutation | novel | c.2482N>G | p.Ile828Val | p.I828V | Q9BYX2 | protein_coding | deleterious(0.03) | benign(0.404) | TCGA-B6-A2IU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| TBC1D2 | SNV | Missense_Mutation | c.670N>A | p.Gly224Ser | p.G224S | Q9BYX2 | protein_coding | tolerated(0.18) | benign(0.007) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| TBC1D2 | SNV | Missense_Mutation | c.542N>A | p.Leu181Gln | p.L181Q | Q9BYX2 | protein_coding | deleterious(0.01) | probably_damaging(0.95) | TCGA-E9-A243-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | PD | |
| TBC1D2 | insertion | Frame_Shift_Ins | novel | c.1139_1140insTTCC | p.Glu380AspfsTer45 | p.E380Dfs*45 | Q9BYX2 | protein_coding | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |||
| TBC1D2 | deletion | Frame_Shift_Del | novel | c.1415delA | p.Asn472ThrfsTer22 | p.N472Tfs*22 | Q9BYX2 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| TBC1D2 | SNV | Missense_Mutation | novel | c.2255N>T | p.Thr752Met | p.T752M | Q9BYX2 | protein_coding | tolerated(0.09) | possibly_damaging(0.557) | 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 |
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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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