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Gene: LAMTOR4 |
Gene summary for LAMTOR4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LAMTOR4 | Gene ID | 389541 |
| Gene name | late endosomal/lysosomal adaptor, MAPK and MTOR activator 4 | |
| Gene Alias | C7orf59 | |
| Cytomap | 7q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | Q0VGL1 |
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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 |
| 389541 | LAMTOR4 | CA_HPV_1 | Human | Cervix | CC | 1.38e-08 | -2.33e-01 | 0.0264 |
| 389541 | LAMTOR4 | CA_HPV_3 | Human | Cervix | CC | 1.07e-03 | 9.05e-02 | 0.0414 |
| 389541 | LAMTOR4 | CCI_1 | Human | Cervix | CC | 1.28e-07 | -6.86e-01 | 0.528 |
| 389541 | LAMTOR4 | CCI_2 | Human | Cervix | CC | 3.01e-02 | -4.93e-01 | 0.5249 |
| 389541 | LAMTOR4 | CCI_3 | Human | Cervix | CC | 1.27e-10 | -7.04e-01 | 0.516 |
| 389541 | LAMTOR4 | CCII_1 | Human | Cervix | CC | 5.94e-28 | -8.74e-01 | 0.3249 |
| 389541 | LAMTOR4 | Tumor | Human | Cervix | CC | 1.60e-02 | -2.19e-01 | 0.1241 |
| 389541 | LAMTOR4 | sample3 | Human | Cervix | CC | 3.05e-09 | -2.51e-01 | 0.1387 |
| 389541 | LAMTOR4 | H2 | Human | Cervix | HSIL_HPV | 3.54e-09 | -4.20e-01 | 0.0632 |
| 389541 | LAMTOR4 | L1 | Human | Cervix | CC | 1.12e-12 | -2.95e-01 | 0.0802 |
| 389541 | LAMTOR4 | T1 | Human | Cervix | CC | 5.44e-04 | -3.71e-01 | 0.0918 |
| 389541 | LAMTOR4 | T3 | Human | Cervix | CC | 4.31e-10 | -2.71e-01 | 0.1389 |
| 389541 | LAMTOR4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 7.95e-10 | 1.94e-01 | 0.0155 |
| 389541 | LAMTOR4 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.69e-05 | 4.68e-01 | -0.1808 |
| 389541 | LAMTOR4 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.21e-19 | 6.59e-01 | -0.1954 |
| 389541 | LAMTOR4 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.34e-02 | 8.38e-01 | -0.2602 |
| 389541 | LAMTOR4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.62e-04 | 5.12e-01 | -0.1207 |
| 389541 | LAMTOR4 | HTA11_696_2000001011 | Human | Colorectum | AD | 5.64e-16 | 5.46e-01 | -0.1464 |
| 389541 | LAMTOR4 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.97e-06 | 3.26e-01 | -0.1001 |
| 389541 | LAMTOR4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.12e-07 | 5.33e-01 | -0.059 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00011017 | Endometrium | AEH | response to acid chemical | 28/2100 | 135/18723 | 9.24e-04 | 8.43e-03 | 28 |
| GO:00432005 | Endometrium | AEH | response to amino acid | 24/2100 | 116/18723 | 2.14e-03 | 1.65e-02 | 24 |
| GO:00726656 | Endometrium | AEH | protein localization to vacuole | 16/2100 | 67/18723 | 2.52e-03 | 1.87e-02 | 16 |
| GO:00712302 | Endometrium | AEH | cellular response to amino acid stimulus | 16/2100 | 71/18723 | 4.68e-03 | 2.99e-02 | 16 |
| GO:00712293 | Endometrium | AEH | cellular response to acid chemical | 17/2100 | 80/18723 | 6.76e-03 | 3.94e-02 | 17 |
| GO:003253516 | Endometrium | EEC | regulation of cellular component size | 79/2168 | 383/18723 | 1.98e-07 | 8.93e-06 | 79 |
| GO:000836111 | Endometrium | EEC | regulation of cell size | 39/2168 | 181/18723 | 8.72e-05 | 1.24e-03 | 39 |
| GO:000110113 | Endometrium | EEC | response to acid chemical | 29/2168 | 135/18723 | 6.98e-04 | 6.68e-03 | 29 |
| GO:004320012 | Endometrium | EEC | response to amino acid | 25/2168 | 116/18723 | 1.50e-03 | 1.21e-02 | 25 |
| GO:007123011 | Endometrium | EEC | cellular response to amino acid stimulus | 17/2168 | 71/18723 | 2.57e-03 | 1.86e-02 | 17 |
| GO:007266513 | Endometrium | EEC | protein localization to vacuole | 16/2168 | 67/18723 | 3.48e-03 | 2.35e-02 | 16 |
| GO:007122911 | Endometrium | EEC | cellular response to acid chemical | 18/2168 | 80/18723 | 4.02e-03 | 2.66e-02 | 18 |
| GO:003253520 | Esophagus | ESCC | regulation of cellular component size | 227/8552 | 383/18723 | 4.77e-08 | 8.60e-07 | 227 |
| GO:00726659 | Esophagus | ESCC | protein localization to vacuole | 52/8552 | 67/18723 | 9.14e-08 | 1.52e-06 | 52 |
| GO:00432007 | Esophagus | ESCC | response to amino acid | 74/8552 | 116/18723 | 6.23e-05 | 4.76e-04 | 74 |
| GO:000110110 | Esophagus | ESCC | response to acid chemical | 84/8552 | 135/18723 | 7.70e-05 | 5.74e-04 | 84 |
| GO:00319294 | Esophagus | ESCC | TOR signaling | 79/8552 | 126/18723 | 8.57e-05 | 6.21e-04 | 79 |
| GO:00614626 | Esophagus | ESCC | protein localization to lysosome | 34/8552 | 46/18723 | 9.39e-05 | 6.70e-04 | 34 |
| GO:00712305 | Esophagus | ESCC | cellular response to amino acid stimulus | 48/8552 | 71/18723 | 1.55e-04 | 1.03e-03 | 48 |
| GO:00083619 | Esophagus | ESCC | regulation of cell size | 107/8552 | 181/18723 | 1.81e-04 | 1.16e-03 | 107 |
| 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 |
| 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 |
| 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 |
| LAMTOR4 | SNV | Missense_Mutation | c.49N>C | p.Gly17Arg | p.G17R | Q0VGL1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A2LX-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| LAMTOR4 | SNV | Missense_Mutation | novel | c.194N>A | p.Arg65His | p.R65H | Q0VGL1 | protein_coding | tolerated(0.06) | benign(0.067) | TCGA-VS-A8EJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| LAMTOR4 | SNV | Missense_Mutation | novel | c.287N>T | p.Pro96Leu | p.P96L | Q0VGL1 | protein_coding | tolerated(0.06) | probably_damaging(0.998) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| LAMTOR4 | SNV | Missense_Mutation | c.76N>T | p.Val26Leu | p.V26L | Q0VGL1 | protein_coding | deleterious(0.03) | benign(0.269) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LAMTOR4 | SNV | Missense_Mutation | novel | c.203N>G | p.Val68Gly | p.V68G | Q0VGL1 | protein_coding | deleterious(0.01) | benign(0.022) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LAMTOR4 | SNV | Missense_Mutation | c.248N>T | p.Arg83Met | p.R83M | Q0VGL1 | protein_coding | deleterious(0) | benign(0.416) | TCGA-D1-A103-01 | 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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