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Gene: LETM1 |
Gene summary for LETM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LETM1 | Gene ID | 3954 |
| Gene name | leucine zipper and EF-hand containing transmembrane protein 1 | |
| Gene Alias | SLC55A1 | |
| Cytomap | 4p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0006810 | UniProtAcc | O95202 |
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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 |
| 3954 | LETM1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.38e-08 | 6.55e-01 | -0.1808 |
| 3954 | LETM1 | HTA11_347_2000001011 | Human | Colorectum | AD | 4.16e-16 | 6.17e-01 | -0.1954 |
| 3954 | LETM1 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.19e-02 | 7.19e-01 | -0.2602 |
| 3954 | LETM1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.60e-02 | 3.06e-01 | -0.1207 |
| 3954 | LETM1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.14e-04 | 5.41e-01 | -0.1526 |
| 3954 | LETM1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.34e-11 | 4.96e-01 | -0.1464 |
| 3954 | LETM1 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.11e-06 | 3.20e-01 | -0.1001 |
| 3954 | LETM1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.61e-07 | 4.93e-01 | -0.059 |
| 3954 | LETM1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 7.28e-07 | 4.24e-01 | 0.3859 |
| 3954 | LETM1 | A015-C-203 | Human | Colorectum | FAP | 3.63e-02 | -1.39e-01 | -0.1294 |
| 3954 | LETM1 | A002-C-205 | Human | Colorectum | FAP | 2.28e-03 | -1.02e-01 | -0.1236 |
| 3954 | LETM1 | A015-C-006 | Human | Colorectum | FAP | 1.58e-02 | -1.24e-01 | -0.0994 |
| 3954 | LETM1 | A002-C-114 | Human | Colorectum | FAP | 1.57e-02 | -1.28e-01 | -0.1561 |
| 3954 | LETM1 | A015-C-104 | Human | Colorectum | FAP | 8.40e-04 | -1.18e-01 | -0.1899 |
| 3954 | LETM1 | A002-C-116 | Human | Colorectum | FAP | 4.59e-05 | -1.79e-01 | -0.0452 |
| 3954 | LETM1 | A018-E-020 | Human | Colorectum | FAP | 3.19e-03 | -1.55e-01 | -0.2034 |
| 3954 | LETM1 | LZE20T | Human | Esophagus | ESCC | 1.55e-03 | 2.02e-01 | 0.0662 |
| 3954 | LETM1 | LZE22T | Human | Esophagus | ESCC | 1.57e-02 | 3.04e-01 | 0.068 |
| 3954 | LETM1 | LZE24T | Human | Esophagus | ESCC | 2.11e-10 | 2.26e-01 | 0.0596 |
| 3954 | LETM1 | P1T-E | Human | Esophagus | ESCC | 3.31e-05 | 2.89e-01 | 0.0875 |
| Page: 1 2 3 4 5 6 |
| 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:0006839 | Colorectum | AD | mitochondrial transport | 102/3918 | 254/18723 | 1.87e-12 | 3.08e-10 | 102 |
| GO:1990542 | Colorectum | AD | mitochondrial transmembrane transport | 47/3918 | 102/18723 | 1.09e-08 | 6.52e-07 | 47 |
| GO:0007006 | Colorectum | AD | mitochondrial membrane organization | 48/3918 | 116/18723 | 4.53e-07 | 1.72e-05 | 48 |
| GO:0062197 | Colorectum | AD | cellular response to chemical stress | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
| GO:0007007 | Colorectum | AD | inner mitochondrial membrane organization | 18/3918 | 38/18723 | 2.45e-04 | 3.09e-03 | 18 |
| GO:0051560 | Colorectum | AD | mitochondrial calcium ion homeostasis | 13/3918 | 26/18723 | 9.41e-04 | 8.92e-03 | 13 |
| GO:0006851 | Colorectum | AD | mitochondrial calcium ion transmembrane transport | 10/3918 | 20/18723 | 3.67e-03 | 2.60e-02 | 10 |
| GO:0051651 | Colorectum | AD | maintenance of location in cell | 61/3918 | 214/18723 | 5.02e-03 | 3.37e-02 | 61 |
| GO:0071472 | Colorectum | AD | cellular response to salt stress | 7/3918 | 12/18723 | 5.09e-03 | 3.38e-02 | 7 |
| GO:00068391 | Colorectum | SER | mitochondrial transport | 87/2897 | 254/18723 | 7.91e-14 | 3.03e-11 | 87 |
| GO:19905421 | Colorectum | SER | mitochondrial transmembrane transport | 42/2897 | 102/18723 | 3.65e-10 | 4.77e-08 | 42 |
| GO:00621971 | Colorectum | SER | cellular response to chemical stress | 87/2897 | 337/18723 | 5.33e-07 | 2.59e-05 | 87 |
| GO:00070061 | Colorectum | SER | mitochondrial membrane organization | 38/2897 | 116/18723 | 2.66e-06 | 1.10e-04 | 38 |
| GO:00068511 | Colorectum | SER | mitochondrial calcium ion transmembrane transport | 10/2897 | 20/18723 | 3.20e-04 | 5.15e-03 | 10 |
| GO:00515601 | Colorectum | SER | mitochondrial calcium ion homeostasis | 11/2897 | 26/18723 | 9.60e-04 | 1.15e-02 | 11 |
| GO:00070071 | Colorectum | SER | inner mitochondrial membrane organization | 14/2897 | 38/18723 | 1.06e-03 | 1.23e-02 | 14 |
| GO:0006970 | Colorectum | SER | response to osmotic stress | 23/2897 | 84/18723 | 3.61e-03 | 3.03e-02 | 23 |
| GO:00714721 | Colorectum | SER | cellular response to salt stress | 6/2897 | 12/18723 | 5.42e-03 | 4.03e-02 | 6 |
| GO:00516511 | Colorectum | SER | maintenance of location in cell | 47/2897 | 214/18723 | 7.20e-03 | 4.99e-02 | 47 |
| GO:00068392 | Colorectum | MSS | mitochondrial transport | 93/3467 | 254/18723 | 6.14e-12 | 9.82e-10 | 93 |
| Page: 1 2 3 4 5 6 7 |
| 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 |
| LETM1 | SNV | Missense_Mutation | c.1145N>A | p.Arg382Gln | p.R382Q | O95202 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| LETM1 | SNV | Missense_Mutation | c.721G>A | p.Glu241Lys | p.E241K | O95202 | protein_coding | deleterious(0.01) | benign(0.327) | TCGA-A2-A0T0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| LETM1 | SNV | Missense_Mutation | c.1845G>A | p.Met615Ile | p.M615I | O95202 | protein_coding | deleterious(0.03) | probably_damaging(0.914) | TCGA-AR-A24R-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| LETM1 | SNV | Missense_Mutation | c.730T>A | p.Ser244Thr | p.S244T | O95202 | protein_coding | tolerated(0.29) | probably_damaging(0.996) | TCGA-BH-A0DH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| LETM1 | SNV | Missense_Mutation | c.870C>A | p.Phe290Leu | p.F290L | O95202 | protein_coding | tolerated(0.08) | possibly_damaging(0.761) | TCGA-BH-A0E2-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD | |
| LETM1 | SNV | Missense_Mutation | c.1605G>C | p.Leu535Phe | p.L535F | O95202 | protein_coding | tolerated(0.05) | benign(0.143) | TCGA-GM-A2D9-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
| LETM1 | insertion | Frame_Shift_Ins | rs745839823 | c.432_433insC | p.Ala145ArgfsTer61 | p.A145Rfs*61 | O95202 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| LETM1 | deletion | Frame_Shift_Del | novel | c.1012delN | p.Ile338SerfsTer18 | p.I338Sfs*18 | O95202 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| LETM1 | deletion | Frame_Shift_Del | novel | c.635delN | p.Phe212SerfsTer18 | p.F212Sfs*18 | O95202 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| LETM1 | SNV | Missense_Mutation | rs577048812 | c.1033C>T | p.Arg345Cys | p.R345C | O95202 | protein_coding | deleterious(0) | benign(0.364) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 |
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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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