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Gene: TOM1L1 |
Gene summary for TOM1L1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TOM1L1 | Gene ID | 10040 |
| Gene name | target of myb1 like 1 membrane trafficking protein | |
| Gene Alias | SRCASM | |
| Cytomap | 17q22 | |
| Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | O75674 |
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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 |
| 10040 | TOM1L1 | HTA11_866_3004761011 | Human | Colorectum | AD | 5.61e-04 | -3.41e-01 | 0.096 |
| 10040 | TOM1L1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.11e-06 | -3.11e-01 | 0.0674 |
| 10040 | TOM1L1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.46e-04 | -2.97e-01 | 0.3859 |
| 10040 | TOM1L1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 2.79e-08 | -3.18e-01 | 0.3005 |
| 10040 | TOM1L1 | F007 | Human | Colorectum | FAP | 6.40e-03 | -2.59e-01 | 0.1176 |
| 10040 | TOM1L1 | A001-C-207 | Human | Colorectum | FAP | 1.20e-07 | -3.92e-01 | 0.1278 |
| 10040 | TOM1L1 | A015-C-203 | Human | Colorectum | FAP | 1.68e-22 | -4.26e-01 | -0.1294 |
| 10040 | TOM1L1 | A015-C-204 | Human | Colorectum | FAP | 4.31e-11 | -4.07e-01 | -0.0228 |
| 10040 | TOM1L1 | A014-C-040 | Human | Colorectum | FAP | 6.92e-05 | -4.40e-01 | -0.1184 |
| 10040 | TOM1L1 | A002-C-201 | Human | Colorectum | FAP | 3.64e-15 | -3.88e-01 | 0.0324 |
| 10040 | TOM1L1 | A002-C-203 | Human | Colorectum | FAP | 6.24e-07 | -2.57e-01 | 0.2786 |
| 10040 | TOM1L1 | A001-C-119 | Human | Colorectum | FAP | 8.92e-07 | -4.28e-01 | -0.1557 |
| 10040 | TOM1L1 | A001-C-108 | Human | Colorectum | FAP | 2.96e-18 | -3.83e-01 | -0.0272 |
| 10040 | TOM1L1 | A002-C-205 | Human | Colorectum | FAP | 2.68e-23 | -4.99e-01 | -0.1236 |
| 10040 | TOM1L1 | A001-C-104 | Human | Colorectum | FAP | 4.46e-08 | -3.15e-01 | 0.0184 |
| 10040 | TOM1L1 | A015-C-005 | Human | Colorectum | FAP | 5.31e-04 | -2.13e-01 | -0.0336 |
| 10040 | TOM1L1 | A015-C-006 | Human | Colorectum | FAP | 7.79e-13 | -3.80e-01 | -0.0994 |
| 10040 | TOM1L1 | A015-C-106 | Human | Colorectum | FAP | 2.75e-17 | -3.55e-01 | -0.0511 |
| 10040 | TOM1L1 | A002-C-114 | Human | Colorectum | FAP | 1.90e-18 | -4.80e-01 | -0.1561 |
| 10040 | TOM1L1 | A015-C-104 | Human | Colorectum | FAP | 2.65e-26 | -4.60e-01 | -0.1899 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:0010639 | Colorectum | AD | negative regulation of organelle organization | 114/3918 | 348/18723 | 1.41e-07 | 6.49e-06 | 114 |
| GO:0046777 | Colorectum | AD | protein autophosphorylation | 74/3918 | 227/18723 | 2.48e-05 | 4.76e-04 | 74 |
| GO:0033674 | Colorectum | AD | positive regulation of kinase activity | 131/3918 | 467/18723 | 1.28e-04 | 1.85e-03 | 131 |
| GO:0045860 | Colorectum | AD | positive regulation of protein kinase activity | 107/3918 | 386/18723 | 8.01e-04 | 7.92e-03 | 107 |
| 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:00106392 | Colorectum | MSS | negative regulation of organelle organization | 102/3467 | 348/18723 | 5.36e-07 | 2.05e-05 | 102 |
| GO:00336742 | Colorectum | MSS | positive regulation of kinase activity | 122/3467 | 467/18723 | 2.50e-05 | 5.21e-04 | 122 |
| GO:00458602 | Colorectum | MSS | positive regulation of protein kinase activity | 102/3467 | 386/18723 | 6.93e-05 | 1.20e-03 | 102 |
| GO:00467772 | Colorectum | MSS | protein autophosphorylation | 63/3467 | 227/18723 | 3.96e-04 | 4.91e-03 | 63 |
| 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:00467773 | Colorectum | FAP | protein autophosphorylation | 52/2622 | 227/18723 | 1.88e-04 | 2.76e-03 | 52 |
| GO:00458604 | Colorectum | FAP | positive regulation of protein kinase activity | 77/2622 | 386/18723 | 7.31e-04 | 7.81e-03 | 77 |
| GO:00336744 | Colorectum | FAP | positive regulation of kinase activity | 89/2622 | 467/18723 | 1.33e-03 | 1.22e-02 | 89 |
| 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:00458605 | Colorectum | CRC | positive regulation of protein kinase activity | 67/2078 | 386/18723 | 1.34e-04 | 2.55e-03 | 67 |
| GO:00336745 | Colorectum | CRC | positive regulation of kinase activity | 77/2078 | 467/18723 | 2.42e-04 | 4.00e-03 | 77 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| TOM1L1 | SNV | Missense_Mutation | c.592N>T | p.Val198Phe | p.V198F | O75674 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-AR-A24H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| TOM1L1 | SNV | Missense_Mutation | novel | c.1231N>G | p.Thr411Ala | p.T411A | O75674 | protein_coding | tolerated(0.34) | benign(0.003) | TCGA-JL-A3YW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TOM1L1 | insertion | Frame_Shift_Ins | novel | c.564_565insAGCTTAAGAATTGTGTTTTCGGCTGGGTGCGGTG | p.Ala189SerfsTer31 | p.A189Sfs*31 | O75674 | protein_coding | TCGA-A8-A07U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | SD | ||
| TOM1L1 | deletion | Frame_Shift_Del | novel | c.970delN | p.Arg325GlyfsTer13 | p.R325Gfs*13 | O75674 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| TOM1L1 | SNV | Missense_Mutation | novel | c.1122N>T | p.Glu374Asp | p.E374D | O75674 | protein_coding | tolerated(0.07) | benign(0.001) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TOM1L1 | SNV | Missense_Mutation | c.1095N>C | p.Met365Ile | p.M365I | O75674 | protein_coding | tolerated(0.09) | benign(0.01) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| TOM1L1 | SNV | Missense_Mutation | c.820G>A | p.Glu274Lys | p.E274K | O75674 | protein_coding | tolerated(0.08) | probably_damaging(0.969) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| TOM1L1 | SNV | Missense_Mutation | novel | c.439G>T | p.Val147Phe | p.V147F | O75674 | protein_coding | tolerated(0.09) | benign(0.026) | TCGA-VS-A9U6-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| TOM1L1 | SNV | Missense_Mutation | c.286N>A | p.Phe96Ile | p.F96I | O75674 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| TOM1L1 | SNV | Missense_Mutation | novel | c.366N>A | p.Phe122Leu | p.F122L | O75674 | protein_coding | tolerated(0.74) | benign(0.141) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <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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