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Gene: LTN1 |
Gene summary for LTN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LTN1 | Gene ID | 26046 |
| Gene name | listerin E3 ubiquitin protein ligase 1 | |
| Gene Alias | C21orf10 | |
| Cytomap | 21q21.3 | |
| Gene Type | protein-coding | GO ID | GO:0006412 | UniProtAcc | O94822 |
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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 |
| 26046 | LTN1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.40e-19 | -4.87e-01 | 0.0155 |
| 26046 | LTN1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.00e-07 | -4.35e-01 | -0.1808 |
| 26046 | LTN1 | HTA11_2951_2000001011 | Human | Colorectum | AD | 9.40e-03 | -5.04e-01 | 0.0216 |
| 26046 | LTN1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.45e-03 | -4.02e-01 | -0.0811 |
| 26046 | LTN1 | HTA11_78_2000001011 | Human | Colorectum | AD | 4.01e-02 | -2.77e-01 | -0.1088 |
| 26046 | LTN1 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.65e-03 | -2.30e-01 | -0.1954 |
| 26046 | LTN1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.39e-07 | -4.66e-01 | -0.1207 |
| 26046 | LTN1 | HTA11_83_2000001011 | Human | Colorectum | SER | 3.66e-04 | -4.43e-01 | -0.1526 |
| 26046 | LTN1 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.82e-08 | -3.90e-01 | -0.1464 |
| 26046 | LTN1 | HTA11_866_2000001011 | Human | Colorectum | AD | 8.96e-07 | -3.90e-01 | -0.1001 |
| 26046 | LTN1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 6.22e-08 | -4.00e-01 | -0.059 |
| 26046 | LTN1 | HTA11_546_2000001011 | Human | Colorectum | AD | 4.85e-03 | -4.34e-01 | -0.0842 |
| 26046 | LTN1 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.35e-14 | -4.65e-01 | 0.096 |
| 26046 | LTN1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 9.40e-03 | -5.04e-01 | 0.0446 |
| 26046 | LTN1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 3.26e-05 | -4.10e-01 | 0.0338 |
| 26046 | LTN1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.72e-08 | -4.36e-01 | 0.0674 |
| 26046 | LTN1 | HTA11_6818_2000001011 | Human | Colorectum | AD | 8.36e-04 | -4.83e-01 | 0.0112 |
| 26046 | LTN1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 5.45e-08 | -4.90e-01 | 0.0588 |
| 26046 | LTN1 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.17e-08 | -3.86e-01 | 0.294 |
| 26046 | LTN1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.95e-04 | -3.45e-01 | 0.3859 |
| 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 | ||
| 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:0010498 | Colorectum | AD | proteasomal protein catabolic process | 174/3918 | 490/18723 | 3.18e-14 | 7.66e-12 | 174 |
| GO:0043161 | Colorectum | AD | proteasome-mediated ubiquitin-dependent protein catabolic process | 141/3918 | 412/18723 | 1.77e-10 | 1.68e-08 | 141 |
| GO:0006417 | Colorectum | AD | regulation of translation | 141/3918 | 468/18723 | 1.32e-06 | 4.22e-05 | 141 |
| GO:0051865 | Colorectum | AD | protein autoubiquitination | 28/3918 | 73/18723 | 4.87e-04 | 5.30e-03 | 28 |
| GO:0006414 | Colorectum | AD | translational elongation | 21/3918 | 55/18723 | 2.53e-03 | 1.93e-02 | 21 |
| GO:00104981 | Colorectum | SER | proteasomal protein catabolic process | 132/2897 | 490/18723 | 3.08e-11 | 5.55e-09 | 132 |
| GO:00431611 | Colorectum | SER | proteasome-mediated ubiquitin-dependent protein catabolic process | 105/2897 | 412/18723 | 7.48e-08 | 4.70e-06 | 105 |
| GO:00064171 | Colorectum | SER | regulation of translation | 100/2897 | 468/18723 | 3.76e-04 | 5.74e-03 | 100 |
| GO:00064141 | Colorectum | SER | translational elongation | 17/2897 | 55/18723 | 3.00e-03 | 2.65e-02 | 17 |
| GO:00104982 | Colorectum | MSS | proteasomal protein catabolic process | 157/3467 | 490/18723 | 2.39e-13 | 5.25e-11 | 157 |
| GO:00431612 | Colorectum | MSS | proteasome-mediated ubiquitin-dependent protein catabolic process | 127/3467 | 412/18723 | 7.70e-10 | 6.32e-08 | 127 |
| GO:00064172 | Colorectum | MSS | regulation of translation | 134/3467 | 468/18723 | 4.43e-08 | 2.38e-06 | 134 |
| GO:00518651 | Colorectum | MSS | protein autoubiquitination | 25/3467 | 73/18723 | 1.00e-03 | 1.00e-02 | 25 |
| GO:00064142 | Colorectum | MSS | translational elongation | 19/3467 | 55/18723 | 3.47e-03 | 2.59e-02 | 19 |
| GO:00064174 | Colorectum | FAP | regulation of translation | 111/2622 | 468/18723 | 8.47e-09 | 1.13e-06 | 111 |
| GO:00431614 | Colorectum | FAP | proteasome-mediated ubiquitin-dependent protein catabolic process | 98/2622 | 412/18723 | 5.41e-08 | 4.20e-06 | 98 |
| GO:00104984 | Colorectum | FAP | proteasomal protein catabolic process | 110/2622 | 490/18723 | 2.12e-07 | 1.26e-05 | 110 |
| GO:00518652 | Colorectum | FAP | protein autoubiquitination | 22/2622 | 73/18723 | 2.88e-04 | 3.77e-03 | 22 |
| GO:00064175 | Colorectum | CRC | regulation of translation | 82/2078 | 468/18723 | 1.79e-05 | 5.40e-04 | 82 |
| GO:00431615 | Colorectum | CRC | proteasome-mediated ubiquitin-dependent protein catabolic process | 69/2078 | 412/18723 | 3.16e-04 | 4.90e-03 | 69 |
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| 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 |
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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 |
| LTN1 | SNV | Missense_Mutation | rs763137490 | c.117G>C | p.Gln39His | p.Q39H | O94822 | protein_coding | tolerated_low_confidence(0.07) | benign(0.116) | TCGA-A2-A0CR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| LTN1 | SNV | Missense_Mutation | c.3979N>A | p.Ala1327Thr | p.A1327T | O94822 | protein_coding | tolerated(0.24) | benign(0.005) | TCGA-A2-A0ET-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| LTN1 | SNV | Missense_Mutation | rs147845371 | c.4718C>T | p.Ala1573Val | p.A1573V | O94822 | protein_coding | tolerated(0.09) | benign(0.038) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| LTN1 | SNV | Missense_Mutation | c.2825N>G | p.Leu942Arg | p.L942R | O94822 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-B6-A0RS-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD | |
| LTN1 | SNV | Missense_Mutation | c.1472T>G | p.Val491Gly | p.V491G | O94822 | protein_coding | deleterious(0.01) | possibly_damaging(0.543) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| LTN1 | SNV | Missense_Mutation | c.2724N>G | p.His908Gln | p.H908Q | O94822 | protein_coding | tolerated(0.07) | possibly_damaging(0.586) | TCGA-D8-A1XW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| LTN1 | SNV | Missense_Mutation | c.514C>G | p.Gln172Glu | p.Q172E | O94822 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| LTN1 | insertion | In_Frame_Ins | novel | c.4849_4850insACAGTTTAGTAGGACCAGATTCTTGTCCTG | p.Thr1617delinsAsnSerLeuValGlyProAspSerCysProAla | p.T1617delinsNSLVGPDSCPA | O94822 | protein_coding | TCGA-AO-A03P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | letrozole | PD | ||
| LTN1 | insertion | In_Frame_Ins | novel | c.4667_4668insATGTAT | p.Asn1556delinsLysCysIle | p.N1556delinsKCI | O94822 | protein_coding | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | ||
| LTN1 | insertion | Nonsense_Mutation | novel | c.5017_5018insGACTATAACACTTTAAGTATTGGTCCAGAAGA | p.Lys1673ArgfsTer3 | p.K1673Rfs*3 | O94822 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
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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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