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Gene: LAG3 |
Gene summary for LAG3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LAG3 | Gene ID | 3902 |
| Gene name | lymphocyte activating 3 | |
| Gene Alias | CD223 | |
| Cytomap | 12p13.31 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | P18627 |
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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 |
| 3902 | LAG3 | C21 | Human | Oral cavity | OSCC | 1.30e-20 | 6.51e-01 | 0.2678 |
| 3902 | LAG3 | C30 | Human | Oral cavity | OSCC | 1.79e-02 | 2.11e-01 | 0.3055 |
| 3902 | LAG3 | C38 | Human | Oral cavity | OSCC | 5.51e-08 | 8.31e-01 | 0.172 |
| 3902 | LAG3 | C43 | Human | Oral cavity | OSCC | 8.75e-05 | 1.08e-01 | 0.1704 |
| 3902 | LAG3 | C46 | Human | Oral cavity | OSCC | 6.79e-09 | 2.35e-01 | 0.1673 |
| 3902 | LAG3 | C57 | Human | Oral cavity | OSCC | 3.22e-04 | 2.28e-01 | 0.1679 |
| 3902 | LAG3 | C08 | Human | Oral cavity | OSCC | 8.35e-04 | 1.36e-01 | 0.1919 |
| 3902 | LAG3 | LN22 | Human | Oral cavity | OSCC | 2.85e-06 | 6.89e-01 | 0.1733 |
| 3902 | LAG3 | LN46 | Human | Oral cavity | OSCC | 3.72e-10 | 3.19e-01 | 0.1666 |
| 3902 | LAG3 | LP15 | Human | Oral cavity | LP | 9.93e-03 | 4.04e-01 | 0.2174 |
| 3902 | LAG3 | SYSMH2 | Human | Oral cavity | OSCC | 3.50e-02 | 9.13e-02 | 0.2326 |
| 3902 | LAG3 | SYSMH6 | Human | Oral cavity | OSCC | 1.66e-02 | 1.01e-01 | 0.1275 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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). |
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| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00028317 | Oral cavity | OSCC | regulation of response to biotic stimulus | 177/7305 | 327/18723 | 1.73e-08 | 3.43e-07 | 177 |
| GO:004211016 | Oral cavity | OSCC | T cell activation | 245/7305 | 487/18723 | 2.00e-07 | 3.22e-06 | 245 |
| GO:19031316 | Oral cavity | OSCC | mononuclear cell differentiation | 210/7305 | 426/18723 | 8.44e-06 | 9.02e-05 | 210 |
| GO:00450884 | Oral cavity | OSCC | regulation of innate immune response | 116/7305 | 218/18723 | 1.36e-05 | 1.37e-04 | 116 |
| GO:002240718 | Oral cavity | OSCC | regulation of cell-cell adhesion | 218/7305 | 448/18723 | 1.71e-05 | 1.68e-04 | 218 |
| GO:190370618 | Oral cavity | OSCC | regulation of hemopoiesis | 180/7305 | 367/18723 | 5.16e-05 | 4.30e-04 | 180 |
| GO:005086315 | Oral cavity | OSCC | regulation of T cell activation | 161/7305 | 329/18723 | 1.44e-04 | 1.02e-03 | 161 |
| GO:00321037 | Oral cavity | OSCC | positive regulation of response to external stimulus | 203/7305 | 427/18723 | 1.79e-04 | 1.22e-03 | 203 |
| GO:000715916 | Oral cavity | OSCC | leukocyte cell-cell adhesion | 178/7305 | 371/18723 | 2.44e-04 | 1.57e-03 | 178 |
| GO:00300983 | Oral cavity | OSCC | lymphocyte differentiation | 179/7305 | 374/18723 | 2.74e-04 | 1.74e-03 | 179 |
| GO:190303715 | Oral cavity | OSCC | regulation of leukocyte cell-cell adhesion | 162/7305 | 336/18723 | 3.39e-04 | 2.08e-03 | 162 |
| GO:000268310 | Oral cavity | OSCC | negative regulation of immune system process | 204/7305 | 434/18723 | 3.72e-04 | 2.27e-03 | 204 |
| GO:19021059 | Oral cavity | OSCC | regulation of leukocyte differentiation | 136/7305 | 279/18723 | 5.53e-04 | 3.21e-03 | 136 |
| GO:00302175 | Oral cavity | OSCC | T cell differentiation | 126/7305 | 257/18723 | 6.51e-04 | 3.66e-03 | 126 |
| GO:00071629 | Oral cavity | OSCC | negative regulation of cell adhesion | 145/7305 | 303/18723 | 9.95e-04 | 5.18e-03 | 145 |
| GO:00456194 | Oral cavity | OSCC | regulation of lymphocyte differentiation | 83/7305 | 174/18723 | 1.18e-02 | 4.00e-02 | 83 |
| GO:00313495 | Oral cavity | OSCC | positive regulation of defense response | 127/7305 | 278/18723 | 1.32e-02 | 4.39e-02 | 127 |
| GO:00224086 | Oral cavity | OSCC | negative regulation of cell-cell adhesion | 92/7305 | 196/18723 | 1.41e-02 | 4.64e-02 | 92 |
| GO:004508811 | Oral cavity | LP | regulation of innate immune response | 78/4623 | 218/18723 | 1.57e-04 | 1.78e-03 | 78 |
| GO:000283112 | Oral cavity | LP | regulation of response to biotic stimulus | 109/4623 | 327/18723 | 2.45e-04 | 2.60e-03 | 109 |
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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. |
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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 |
| LAG3 | SNV | Missense_Mutation | c.1079N>T | p.Ser360Leu | p.S360L | P18627 | protein_coding | tolerated(1) | benign(0) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD | |
| LAG3 | SNV | Missense_Mutation | novel | c.799N>G | p.Pro267Ala | p.P267A | P18627 | protein_coding | deleterious(0.01) | possibly_damaging(0.492) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| LAG3 | SNV | Missense_Mutation | c.902N>A | p.Pro301His | p.P301H | P18627 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
| LAG3 | SNV | Missense_Mutation | c.32N>G | p.Phe11Cys | p.F11C | P18627 | protein_coding | deleterious(0) | benign(0.334) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| LAG3 | SNV | Missense_Mutation | rs141308793 | c.1135N>T | p.Arg379Cys | p.R379C | P18627 | protein_coding | deleterious(0) | benign(0.23) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| LAG3 | SNV | Missense_Mutation | novel | c.119C>T | p.Ala40Val | p.A40V | P18627 | protein_coding | tolerated(0.39) | benign(0.003) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| LAG3 | SNV | Missense_Mutation | novel | c.56N>T | p.Pro19Leu | p.P19L | P18627 | protein_coding | deleterious(0) | benign(0.108) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| LAG3 | SNV | Missense_Mutation | c.1535C>T | p.Pro512Leu | p.P512L | P18627 | protein_coding | tolerated_low_confidence(0.14) | benign(0) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LAG3 | SNV | Missense_Mutation | novel | c.847N>T | p.Arg283Cys | p.R283C | P18627 | protein_coding | tolerated(0.12) | possibly_damaging(0.828) | TCGA-AG-3893-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folinic | CR |
| LAG3 | SNV | Missense_Mutation | novel | c.963G>T | p.Glu321Asp | p.E321D | P18627 | protein_coding | tolerated(0.17) | benign(0.08) | TCGA-AG-3898-01 | Colorectum | rectum adenocarcinoma | Male | <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 |
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | FS118 | |||
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | BMS-986016 | RELATLIMAB | 25755681 | |
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | antibody | 336446922 | RELATLIMAB | |
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | IMP-321 | |||
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | IMP-701 | |||
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | GSK2831781 | GSK2831781 | ||
| 3902 | LAG3 | DRUGGABLE GENOME, CLINICALLY ACTIONABLE, EXTERNAL SIDE OF PLASMA MEMBRANE | Anti-LAG3 |
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