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Gene: TOM1L2 |
Gene summary for TOM1L2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TOM1L2 | Gene ID | 146691 |
| Gene name | target of myb1 like 2 membrane trafficking protein | |
| Gene Alias | TOM1L2 | |
| Cytomap | 17p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | Q6ZVM7 |
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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 |
| 146691 | TOM1L2 | CCI_1 | Human | Cervix | CC | 6.30e-16 | 1.05e+00 | 0.528 |
| 146691 | TOM1L2 | CCI_2 | Human | Cervix | CC | 3.91e-11 | 8.89e-01 | 0.5249 |
| 146691 | TOM1L2 | CCI_3 | Human | Cervix | CC | 5.15e-16 | 7.21e-01 | 0.516 |
| 146691 | TOM1L2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.16e-06 | 5.79e-01 | -0.1808 |
| 146691 | TOM1L2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.40e-04 | 5.44e-01 | -0.0811 |
| 146691 | TOM1L2 | HTA11_347_2000001011 | Human | Colorectum | AD | 5.79e-11 | 5.90e-01 | -0.1954 |
| 146691 | TOM1L2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.78e-02 | 7.54e-01 | -0.2196 |
| 146691 | TOM1L2 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.82e-03 | 6.42e-01 | -0.1526 |
| 146691 | TOM1L2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.03e-08 | 7.63e-01 | -0.059 |
| 146691 | TOM1L2 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.28e-02 | -1.92e-01 | 0.294 |
| 146691 | TOM1L2 | A015-C-203 | Human | Colorectum | FAP | 1.86e-24 | -3.60e-01 | -0.1294 |
| 146691 | TOM1L2 | A015-C-204 | Human | Colorectum | FAP | 2.19e-03 | -2.52e-01 | -0.0228 |
| 146691 | TOM1L2 | A002-C-201 | Human | Colorectum | FAP | 6.86e-08 | -2.53e-01 | 0.0324 |
| 146691 | TOM1L2 | A002-C-203 | Human | Colorectum | FAP | 1.11e-02 | -9.96e-02 | 0.2786 |
| 146691 | TOM1L2 | A001-C-119 | Human | Colorectum | FAP | 2.98e-02 | -2.28e-01 | -0.1557 |
| 146691 | TOM1L2 | A001-C-108 | Human | Colorectum | FAP | 2.70e-10 | -2.39e-01 | -0.0272 |
| 146691 | TOM1L2 | A002-C-205 | Human | Colorectum | FAP | 1.59e-15 | -3.66e-01 | -0.1236 |
| 146691 | TOM1L2 | A015-C-005 | Human | Colorectum | FAP | 6.54e-06 | -3.48e-01 | -0.0336 |
| 146691 | TOM1L2 | A015-C-006 | Human | Colorectum | FAP | 5.42e-12 | -4.62e-01 | -0.0994 |
| 146691 | TOM1L2 | A015-C-106 | Human | Colorectum | FAP | 4.18e-07 | -2.19e-01 | -0.0511 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00073466 | Cervix | CC | regulation of mitotic cell cycle | 88/2311 | 457/18723 | 1.26e-05 | 2.60e-04 | 88 |
| GO:00106399 | Cervix | CC | negative regulation of organelle organization | 68/2311 | 348/18723 | 7.40e-05 | 1.03e-03 | 68 |
| GO:00457862 | Cervix | CC | negative regulation of cell cycle | 67/2311 | 385/18723 | 2.21e-03 | 1.59e-02 | 67 |
| GO:00459302 | Cervix | CC | negative regulation of mitotic cell cycle | 44/2311 | 235/18723 | 3.02e-03 | 1.99e-02 | 44 |
| GO:01400143 | Cervix | CC | mitotic nuclear division | 50/2311 | 287/18723 | 7.27e-03 | 3.91e-02 | 50 |
| GO:00109482 | Cervix | CC | negative regulation of cell cycle process | 51/2311 | 294/18723 | 7.35e-03 | 3.94e-02 | 51 |
| GO:00482851 | Cervix | CC | organelle fission | 78/2311 | 488/18723 | 9.70e-03 | 4.79e-02 | 78 |
| GO:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0007346 | Colorectum | AD | regulation of mitotic cell cycle | 119/3918 | 457/18723 | 4.60e-03 | 3.14e-02 | 119 |
| GO:0140014 | Colorectum | AD | mitotic nuclear division | 78/3918 | 287/18723 | 6.48e-03 | 4.05e-02 | 78 |
| GO:00106391 | Colorectum | SER | negative regulation of organelle organization | 90/2897 | 348/18723 | 3.14e-07 | 1.69e-05 | 90 |
| GO:00106392 | Colorectum | MSS | negative regulation of organelle organization | 102/3467 | 348/18723 | 5.36e-07 | 2.05e-05 | 102 |
| GO:00073461 | Colorectum | MSS | regulation of mitotic cell cycle | 108/3467 | 457/18723 | 3.30e-03 | 2.50e-02 | 108 |
| GO:01400141 | Colorectum | MSS | mitotic nuclear division | 70/3467 | 287/18723 | 7.48e-03 | 4.72e-02 | 70 |
| GO:00106393 | Colorectum | FAP | negative regulation of organelle organization | 80/2622 | 348/18723 | 3.62e-06 | 1.27e-04 | 80 |
| GO:00073462 | Colorectum | FAP | regulation of mitotic cell cycle | 85/2622 | 457/18723 | 3.41e-03 | 2.48e-02 | 85 |
| GO:00106394 | Colorectum | CRC | negative regulation of organelle organization | 63/2078 | 348/18723 | 6.09e-05 | 1.35e-03 | 63 |
| GO:001063920 | Esophagus | HGIN | negative regulation of organelle organization | 79/2587 | 348/18723 | 4.12e-06 | 1.37e-04 | 79 |
| GO:000734610 | Esophagus | HGIN | regulation of mitotic cell cycle | 98/2587 | 457/18723 | 4.39e-06 | 1.42e-04 | 98 |
| GO:01400146 | Esophagus | HGIN | mitotic nuclear division | 61/2587 | 287/18723 | 3.38e-04 | 5.55e-03 | 61 |
| 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 |
| 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 |
| TOM1L2 | SNV | Missense_Mutation | c.812N>A | p.Arg271His | p.R271H | Q6ZVM7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TOM1L2 | insertion | Frame_Shift_Ins | novel | c.995_996insGGTGGGAAGATCACTTGAGGCCAGGTGTTTGAGACCAG | p.Asp332GlufsTer23 | p.D332Efs*23 | Q6ZVM7 | protein_coding | TCGA-A8-A0A2-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TOM1L2 | insertion | In_Frame_Ins | novel | c.965_966insTGG | p.Leu322_Asn323insGly | p.L322_N323insG | Q6ZVM7 | protein_coding | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| TOM1L2 | insertion | Frame_Shift_Ins | novel | c.963_964insATATCTACAGAGGG | p.Leu322IlefsTer6 | p.L322Ifs*6 | Q6ZVM7 | protein_coding | TCGA-AN-A0FK-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
| TOM1L2 | SNV | Missense_Mutation | c.1289N>T | p.Ala430Val | p.A430V | Q6ZVM7 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TOM1L2 | SNV | Missense_Mutation | novel | c.1400N>T | p.Arg467Ile | p.R467I | Q6ZVM7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
| TOM1L2 | SNV | Missense_Mutation | c.449A>C | p.Glu150Ala | p.E150A | Q6ZVM7 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
| TOM1L2 | SNV | Missense_Mutation | c.184C>T | p.Arg62Trp | p.R62W | Q6ZVM7 | protein_coding | deleterious(0) | probably_damaging(0.926) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| TOM1L2 | SNV | Missense_Mutation | c.1496N>A | p.Arg499Gln | p.R499Q | Q6ZVM7 | protein_coding | tolerated(0.11) | benign(0.067) | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TOM1L2 | SNV | Missense_Mutation | c.538N>G | p.Arg180Gly | p.R180G | Q6ZVM7 | protein_coding | tolerated(0.46) | benign(0) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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