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Gene: TBC1D12 |
Gene summary for TBC1D12 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TBC1D12 | Gene ID | 23232 |
| Gene name | TBC1 domain family member 12 | |
| Gene Alias | TBC1D12 | |
| Cytomap | 10q23.33 | |
| Gene Type | protein-coding | GO ID | GO:0000045 | UniProtAcc | O60347 |
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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 |
| 23232 | TBC1D12 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.90e-04 | -3.58e-01 | 0.0155 |
| 23232 | TBC1D12 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.37e-03 | 2.55e-01 | -0.1954 |
| 23232 | TBC1D12 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.74e-02 | -4.14e-01 | 0.096 |
| 23232 | TBC1D12 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.19e-07 | -3.84e-01 | 0.294 |
| 23232 | TBC1D12 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.23e-08 | -3.93e-01 | 0.3859 |
| 23232 | TBC1D12 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.68e-15 | -4.94e-01 | 0.3005 |
| 23232 | TBC1D12 | A002-C-010 | Human | Colorectum | FAP | 3.41e-05 | -2.49e-01 | 0.242 |
| 23232 | TBC1D12 | A001-C-207 | Human | Colorectum | FAP | 9.25e-04 | -3.94e-01 | 0.1278 |
| 23232 | TBC1D12 | A015-C-203 | Human | Colorectum | FAP | 4.17e-21 | -4.60e-01 | -0.1294 |
| 23232 | TBC1D12 | A015-C-204 | Human | Colorectum | FAP | 9.26e-03 | -3.39e-01 | -0.0228 |
| 23232 | TBC1D12 | A014-C-040 | Human | Colorectum | FAP | 4.55e-02 | -4.90e-01 | -0.1184 |
| 23232 | TBC1D12 | A002-C-201 | Human | Colorectum | FAP | 2.09e-06 | -3.33e-01 | 0.0324 |
| 23232 | TBC1D12 | A002-C-203 | Human | Colorectum | FAP | 6.78e-08 | -2.87e-01 | 0.2786 |
| 23232 | TBC1D12 | A001-C-119 | Human | Colorectum | FAP | 3.64e-05 | -4.53e-01 | -0.1557 |
| 23232 | TBC1D12 | A001-C-108 | Human | Colorectum | FAP | 4.69e-14 | -4.09e-01 | -0.0272 |
| 23232 | TBC1D12 | A002-C-205 | Human | Colorectum | FAP | 4.05e-11 | -4.05e-01 | -0.1236 |
| 23232 | TBC1D12 | A001-C-104 | Human | Colorectum | FAP | 3.87e-04 | -3.19e-01 | 0.0184 |
| 23232 | TBC1D12 | A015-C-005 | Human | Colorectum | FAP | 1.92e-05 | -4.11e-01 | -0.0336 |
| 23232 | TBC1D12 | A015-C-006 | Human | Colorectum | FAP | 1.22e-08 | -4.60e-01 | -0.0994 |
| 23232 | TBC1D12 | A015-C-106 | Human | Colorectum | FAP | 4.31e-09 | -3.53e-01 | -0.0511 |
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| 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 |
| ∗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:0016236 | Colorectum | AD | macroautophagy | 103/3918 | 291/18723 | 6.76e-09 | 4.15e-07 | 103 |
| 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:0007033 | Colorectum | AD | vacuole organization | 53/3918 | 180/18723 | 4.18e-03 | 2.89e-02 | 53 |
| GO:00162362 | Colorectum | MSS | macroautophagy | 93/3467 | 291/18723 | 2.08e-08 | 1.17e-06 | 93 |
| 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:00070331 | Colorectum | MSS | vacuole organization | 48/3467 | 180/18723 | 4.32e-03 | 3.07e-02 | 48 |
| GO:00430873 | Colorectum | FAP | regulation of GTPase activity | 85/2622 | 348/18723 | 1.20e-07 | 7.68e-06 | 85 |
| GO:00162363 | Colorectum | FAP | macroautophagy | 70/2622 | 291/18723 | 2.73e-06 | 1.02e-04 | 70 |
| 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:00162364 | Colorectum | CRC | macroautophagy | 51/2078 | 291/18723 | 6.40e-04 | 8.48e-03 | 51 |
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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 |
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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 |
| TBC1D12 | SNV | Missense_Mutation | c.2095A>T | p.Thr699Ser | p.T699S | O60347 | protein_coding | deleterious(0.01) | probably_damaging(0.925) | TCGA-A1-A0SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| TBC1D12 | SNV | Missense_Mutation | novel | c.2099N>A | p.Gly700Glu | p.G700E | O60347 | protein_coding | deleterious(0.01) | probably_damaging(0.926) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TBC1D12 | SNV | Missense_Mutation | c.1247G>A | p.Arg416His | p.R416H | O60347 | protein_coding | deleterious(0.01) | benign(0.195) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TBC1D12 | SNV | Missense_Mutation | c.1732T>C | p.Tyr578His | p.Y578H | O60347 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| TBC1D12 | SNV | Missense_Mutation | novel | c.1219N>T | p.Pro407Ser | p.P407S | O60347 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-LL-A7SZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| TBC1D12 | insertion | Frame_Shift_Ins | novel | c.2222_2223insAACACAACTAATAAGTGGCAAATTCAGGATTCAAATCCAGG | p.Ile742ThrfsTer31 | p.I742Tfs*31 | O60347 | protein_coding | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | ||
| TBC1D12 | SNV | Missense_Mutation | novel | c.1828G>A | p.Ala610Thr | p.A610T | O60347 | protein_coding | tolerated(0.11) | benign(0.34) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TBC1D12 | SNV | Missense_Mutation | novel | c.382N>G | p.Pro128Ala | p.P128A | O60347 | protein_coding | tolerated_low_confidence(0.23) | benign(0) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TBC1D12 | SNV | Missense_Mutation | rs528485236 | c.1619N>A | p.Arg540Gln | p.R540Q | O60347 | protein_coding | deleterious(0.04) | possibly_damaging(0.459) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| TBC1D12 | SNV | Missense_Mutation | rs757453586 | c.1253N>A | p.Arg418Gln | p.R418Q | O60347 | protein_coding | tolerated(0.06) | benign(0.125) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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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