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Gene: LARS |
Gene summary for LARS |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LARS | Gene ID | 51520 |
| Gene name | leucyl-tRNA synthetase 1 | |
| Gene Alias | HSPC192 | |
| Cytomap | 5q32 | |
| Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | B4E266 |
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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 |
| 51520 | LARS | CCI_2 | Human | Cervix | CC | 8.30e-15 | 7.59e-01 | 0.5249 |
| 51520 | LARS | CCI_3 | Human | Cervix | CC | 1.09e-21 | 6.01e-01 | 0.516 |
| 51520 | LARS | Tumor | Human | Cervix | CC | 1.84e-10 | 2.04e-01 | 0.1241 |
| 51520 | LARS | sample1 | Human | Cervix | CC | 6.23e-04 | 1.67e-01 | 0.0959 |
| 51520 | LARS | sample3 | Human | Cervix | CC | 4.20e-07 | 1.61e-01 | 0.1387 |
| 51520 | LARS | H2 | Human | Cervix | HSIL_HPV | 1.49e-13 | 3.43e-01 | 0.0632 |
| 51520 | LARS | T1 | Human | Cervix | CC | 2.25e-06 | 1.69e-01 | 0.0918 |
| 51520 | LARS | T2 | Human | Cervix | CC | 2.38e-14 | 4.72e-01 | 0.0709 |
| 51520 | LARS | T3 | Human | Cervix | CC | 3.84e-11 | 1.88e-01 | 0.1389 |
| 51520 | LARS | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.37e-21 | -5.13e-01 | 0.0155 |
| 51520 | LARS | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.52e-12 | -5.13e-01 | -0.1808 |
| 51520 | LARS | HTA11_2951_2000001011 | Human | Colorectum | AD | 4.93e-02 | -5.13e-01 | 0.0216 |
| 51520 | LARS | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.36e-09 | -5.13e-01 | -0.0811 |
| 51520 | LARS | HTA11_78_2000001011 | Human | Colorectum | AD | 6.93e-15 | -5.13e-01 | -0.1088 |
| 51520 | LARS | HTA11_347_2000001011 | Human | Colorectum | AD | 3.24e-23 | -5.13e-01 | -0.1954 |
| 51520 | LARS | HTA11_3361_2000001011 | Human | Colorectum | AD | 9.60e-10 | -5.13e-01 | -0.1207 |
| 51520 | LARS | HTA11_83_2000001011 | Human | Colorectum | SER | 1.22e-07 | -5.13e-01 | -0.1526 |
| 51520 | LARS | HTA11_696_2000001011 | Human | Colorectum | AD | 2.71e-26 | -5.13e-01 | -0.1464 |
| 51520 | LARS | HTA11_866_2000001011 | Human | Colorectum | AD | 4.93e-21 | -5.13e-01 | -0.1001 |
| 51520 | LARS | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.15e-17 | -5.13e-01 | -0.059 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 | ||
| 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:0032535 | Colorectum | AD | regulation of cellular component size | 142/3918 | 383/18723 | 1.74e-13 | 3.41e-11 | 142 |
| GO:0043087 | Colorectum | AD | regulation of GTPase activity | 110/3918 | 348/18723 | 1.64e-06 | 5.03e-05 | 110 |
| GO:0031667 | Colorectum | AD | response to nutrient levels | 138/3918 | 474/18723 | 1.22e-05 | 2.68e-04 | 138 |
| GO:0042594 | Colorectum | AD | response to starvation | 63/3918 | 197/18723 | 1.77e-04 | 2.38e-03 | 63 |
| GO:0071496 | Colorectum | AD | cellular response to external stimulus | 94/3918 | 320/18723 | 1.98e-04 | 2.64e-03 | 94 |
| GO:0006418 | Colorectum | AD | tRNA aminoacylation for protein translation | 19/3918 | 41/18723 | 2.37e-04 | 3.03e-03 | 19 |
| GO:0009267 | Colorectum | AD | cellular response to starvation | 51/3918 | 156/18723 | 3.90e-04 | 4.44e-03 | 51 |
| GO:0043039 | Colorectum | AD | tRNA aminoacylation | 19/3918 | 44/18723 | 7.13e-04 | 7.21e-03 | 19 |
| GO:0043547 | Colorectum | AD | positive regulation of GTPase activity | 75/3918 | 255/18723 | 7.95e-04 | 7.91e-03 | 75 |
| GO:0008361 | Colorectum | AD | regulation of cell size | 56/3918 | 181/18723 | 9.61e-04 | 9.07e-03 | 56 |
| GO:0043038 | Colorectum | AD | amino acid activation | 19/3918 | 45/18723 | 9.94e-04 | 9.28e-03 | 19 |
| GO:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
| GO:0031668 | Colorectum | AD | cellular response to extracellular stimulus | 71/3918 | 246/18723 | 1.86e-03 | 1.52e-02 | 71 |
| GO:0031669 | Colorectum | AD | cellular response to nutrient levels | 63/3918 | 215/18723 | 2.19e-03 | 1.73e-02 | 63 |
| GO:00325351 | Colorectum | SER | regulation of cellular component size | 115/2897 | 383/18723 | 3.04e-13 | 1.10e-10 | 115 |
| GO:00316671 | Colorectum | SER | response to nutrient levels | 106/2897 | 474/18723 | 3.94e-05 | 1.00e-03 | 106 |
| GO:00064181 | Colorectum | SER | tRNA aminoacylation for protein translation | 17/2897 | 41/18723 | 5.75e-05 | 1.35e-03 | 17 |
| GO:00430391 | Colorectum | SER | tRNA aminoacylation | 17/2897 | 44/18723 | 1.64e-04 | 3.12e-03 | 17 |
| GO:00430381 | Colorectum | SER | amino acid activation | 17/2897 | 45/18723 | 2.25e-04 | 3.91e-03 | 17 |
| GO:00430871 | Colorectum | SER | regulation of GTPase activity | 77/2897 | 348/18723 | 5.90e-04 | 8.07e-03 | 77 |
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| 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 |
| LARS | SNV | Missense_Mutation | c.944N>A | p.Gly315Glu | p.G315E | Q9P2J5 | protein_coding | deleterious(0) | benign(0.391) | TCGA-A2-A0CT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | |
| LARS | SNV | Missense_Mutation | c.1421N>T | p.Glu474Val | p.E474V | Q9P2J5 | protein_coding | deleterious(0) | benign(0.076) | TCGA-A7-A26F-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD | |
| LARS | SNV | Missense_Mutation | c.1633N>A | p.Gln545Lys | p.Q545K | Q9P2J5 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LARS | SNV | Missense_Mutation | c.532N>C | p.Glu178Gln | p.E178Q | Q9P2J5 | protein_coding | tolerated(0.46) | benign(0.038) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| LARS | SNV | Missense_Mutation | c.933N>A | p.Met311Ile | p.M311I | Q9P2J5 | protein_coding | tolerated(0.41) | benign(0) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| LARS | SNV | Missense_Mutation | c.1525N>A | p.Glu509Lys | p.E509K | Q9P2J5 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LARS | deletion | Frame_Shift_Del | novel | c.1147delN | p.Asp383IlefsTer24 | p.D383Ifs*24 | Q9P2J5 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| LARS | SNV | Missense_Mutation | novel | c.2050T>C | p.Tyr684His | p.Y684H | Q9P2J5 | protein_coding | deleterious(0) | probably_damaging(0.984) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LARS | SNV | Missense_Mutation | novel | c.1213G>T | p.Asp405Tyr | p.D405Y | Q9P2J5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LARS | SNV | Missense_Mutation | c.1339N>A | p.Asp447Asn | p.D447N | Q9P2J5 | protein_coding | tolerated(0.23) | benign(0.015) | TCGA-BI-A0VR-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | 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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