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Gene: LAMTOR1 |
Gene summary for LAMTOR1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LAMTOR1 | Gene ID | 55004 |
| Gene name | late endosomal/lysosomal adaptor, MAPK and MTOR activator 1 | |
| Gene Alias | C11orf59 | |
| Cytomap | 11q13.4 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q6IAA8 |
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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 |
| 55004 | LAMTOR1 | GSM4909282 | Human | Breast | IDC | 2.28e-03 | 3.48e-01 | -0.0288 |
| 55004 | LAMTOR1 | GSM4909290 | Human | Breast | IDC | 3.14e-14 | 5.39e-01 | 0.2096 |
| 55004 | LAMTOR1 | GSM4909294 | Human | Breast | IDC | 8.16e-05 | 1.60e-01 | 0.2022 |
| 55004 | LAMTOR1 | GSM4909296 | Human | Breast | IDC | 1.44e-18 | 2.46e-01 | 0.1524 |
| 55004 | LAMTOR1 | GSM4909297 | Human | Breast | IDC | 2.24e-18 | -2.21e-01 | 0.1517 |
| 55004 | LAMTOR1 | GSM4909301 | Human | Breast | IDC | 1.02e-02 | 7.06e-02 | 0.1577 |
| 55004 | LAMTOR1 | GSM4909304 | Human | Breast | IDC | 1.24e-09 | 4.98e-01 | 0.1636 |
| 55004 | LAMTOR1 | GSM4909305 | Human | Breast | IDC | 1.16e-03 | 2.90e-01 | 0.0436 |
| 55004 | LAMTOR1 | GSM4909307 | Human | Breast | IDC | 4.22e-06 | 3.79e-01 | 0.1569 |
| 55004 | LAMTOR1 | GSM4909308 | Human | Breast | IDC | 3.82e-24 | 5.68e-01 | 0.158 |
| 55004 | LAMTOR1 | GSM4909311 | Human | Breast | IDC | 2.42e-35 | -2.77e-01 | 0.1534 |
| 55004 | LAMTOR1 | GSM4909312 | Human | Breast | IDC | 7.15e-19 | 1.16e-01 | 0.1552 |
| 55004 | LAMTOR1 | GSM4909313 | Human | Breast | IDC | 2.85e-05 | 2.46e-01 | 0.0391 |
| 55004 | LAMTOR1 | GSM4909316 | Human | Breast | IDC | 2.46e-07 | 2.54e-01 | 0.21 |
| 55004 | LAMTOR1 | GSM4909319 | Human | Breast | IDC | 7.76e-51 | -6.57e-02 | 0.1563 |
| 55004 | LAMTOR1 | GSM4909320 | Human | Breast | IDC | 9.82e-08 | 1.28e-01 | 0.1575 |
| 55004 | LAMTOR1 | GSM4909321 | Human | Breast | IDC | 3.59e-23 | 1.32e-01 | 0.1559 |
| 55004 | LAMTOR1 | brca2 | Human | Breast | Precancer | 3.20e-07 | 3.74e-01 | -0.024 |
| 55004 | LAMTOR1 | brca3 | Human | Breast | Precancer | 3.67e-02 | 2.72e-01 | -0.0263 |
| 55004 | LAMTOR1 | NCCBC11 | Human | Breast | DCIS | 2.53e-06 | 2.98e-01 | 0.1232 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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 | ||
| 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:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
| GO:00192164 | Breast | Precancer | regulation of lipid metabolic process | 34/1080 | 331/18723 | 8.14e-04 | 9.55e-03 | 34 |
| GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
| GO:00011015 | Breast | Precancer | response to acid chemical | 16/1080 | 135/18723 | 4.85e-03 | 3.67e-02 | 16 |
| GO:001921612 | Breast | IDC | regulation of lipid metabolic process | 45/1434 | 331/18723 | 1.21e-04 | 2.24e-03 | 45 |
| GO:00192184 | Breast | IDC | regulation of steroid metabolic process | 18/1434 | 100/18723 | 5.40e-04 | 6.96e-03 | 18 |
| GO:001604913 | Breast | IDC | cell growth | 56/1434 | 482/18723 | 1.16e-03 | 1.26e-02 | 56 |
| GO:000155813 | Breast | IDC | regulation of cell growth | 49/1434 | 414/18723 | 1.55e-03 | 1.55e-02 | 49 |
| GO:000110112 | Breast | IDC | response to acid chemical | 20/1434 | 135/18723 | 3.28e-03 | 2.75e-02 | 20 |
| GO:00431126 | Breast | IDC | receptor metabolic process | 23/1434 | 166/18723 | 4.04e-03 | 3.25e-02 | 23 |
| GO:00432003 | Breast | IDC | response to amino acid | 17/1434 | 116/18723 | 7.13e-03 | 4.92e-02 | 17 |
| GO:001921621 | Breast | DCIS | regulation of lipid metabolic process | 43/1390 | 331/18723 | 2.37e-04 | 3.71e-03 | 43 |
| GO:001604923 | Breast | DCIS | cell growth | 54/1390 | 482/18723 | 1.60e-03 | 1.59e-02 | 54 |
| GO:000155822 | Breast | DCIS | regulation of cell growth | 47/1390 | 414/18723 | 2.39e-03 | 2.16e-02 | 47 |
| GO:004311213 | Breast | DCIS | receptor metabolic process | 23/1390 | 166/18723 | 2.75e-03 | 2.41e-02 | 23 |
| GO:001921811 | Breast | DCIS | regulation of steroid metabolic process | 16/1390 | 100/18723 | 2.77e-03 | 2.42e-02 | 16 |
| GO:000110121 | Breast | DCIS | response to acid chemical | 19/1390 | 135/18723 | 5.17e-03 | 3.81e-02 | 19 |
| GO:0016197 | Colorectum | AD | endosomal transport | 90/3918 | 230/18723 | 1.88e-10 | 1.73e-08 | 90 |
| GO:0016050 | Colorectum | AD | vesicle organization | 101/3918 | 300/18723 | 1.65e-07 | 7.17e-06 | 101 |
| GO:0043112 | Colorectum | AD | receptor metabolic process | 62/3918 | 166/18723 | 8.18e-07 | 2.85e-05 | 62 |
| 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 |
| hsa04150 | Colorectum | MSS | mTOR signaling pathway | 47/1875 | 156/8465 | 1.19e-02 | 3.99e-02 | 2.44e-02 | 47 |
| hsa041501 | Colorectum | MSS | mTOR signaling pathway | 47/1875 | 156/8465 | 1.19e-02 | 3.99e-02 | 2.44e-02 | 47 |
| hsa041505 | Esophagus | ESCC | mTOR signaling pathway | 98/4205 | 156/8465 | 5.81e-04 | 1.95e-03 | 9.97e-04 | 98 |
| hsa0415013 | Esophagus | ESCC | mTOR signaling pathway | 98/4205 | 156/8465 | 5.81e-04 | 1.95e-03 | 9.97e-04 | 98 |
| hsa041502 | Liver | HCC | mTOR signaling pathway | 95/4020 | 156/8465 | 4.70e-04 | 1.99e-03 | 1.11e-03 | 95 |
| hsa0415011 | Liver | HCC | mTOR signaling pathway | 95/4020 | 156/8465 | 4.70e-04 | 1.99e-03 | 1.11e-03 | 95 |
| hsa041504 | Oral cavity | OSCC | mTOR signaling pathway | 90/3704 | 156/8465 | 2.87e-04 | 9.15e-04 | 4.66e-04 | 90 |
| hsa0415012 | Oral cavity | OSCC | mTOR signaling pathway | 90/3704 | 156/8465 | 2.87e-04 | 9.15e-04 | 4.66e-04 | 90 |
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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. |
| 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 |
| LAMTOR1 | SNV | Missense_Mutation | c.24N>C | p.Glu8Asp | p.E8D | Q6IAA8 | protein_coding | tolerated(0.53) | benign(0) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
| LAMTOR1 | SNV | Missense_Mutation | c.55N>T | p.Arg19Trp | p.R19W | Q6IAA8 | protein_coding | tolerated(0.2) | benign(0.047) | TCGA-CM-6162-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| LAMTOR1 | SNV | Missense_Mutation | rs761347517 | c.271N>T | p.Arg91Cys | p.R91C | Q6IAA8 | protein_coding | tolerated(0.09) | benign(0.018) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAMTOR1 | insertion | Frame_Shift_Ins | novel | c.86dupC | p.Thr30TyrfsTer20 | p.T30Yfs*20 | Q6IAA8 | protein_coding | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LAMTOR1 | SNV | Missense_Mutation | c.272N>A | p.Arg91His | p.R91H | Q6IAA8 | protein_coding | tolerated(0.07) | benign(0.018) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LAMTOR1 | SNV | Missense_Mutation | novel | c.98N>C | p.Leu33Pro | p.L33P | Q6IAA8 | protein_coding | tolerated(0.28) | benign(0) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAMTOR1 | SNV | Missense_Mutation | rs370533903 | c.251N>A | p.Arg84His | p.R84H | Q6IAA8 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAMTOR1 | SNV | Missense_Mutation | rs564426310 | c.136N>A | p.Ala46Thr | p.A46T | Q6IAA8 | protein_coding | tolerated(0.72) | benign(0) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAMTOR1 | SNV | Missense_Mutation | c.272N>A | p.Arg91His | p.R91H | Q6IAA8 | protein_coding | tolerated(0.07) | benign(0.018) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LAMTOR1 | SNV | Missense_Mutation | rs564426310 | c.136G>A | p.Ala46Thr | p.A46T | Q6IAA8 | protein_coding | tolerated(0.72) | benign(0) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid 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 |
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