TissGeneSummary for LGI1 |
Gene summary |
Basic gene information | Gene symbol | LGI1 |
Gene name | leucine-rich, glioma inactivated 1 | |
Synonyms | ADLTE|ADPAEF|ADPEAF|EPITEMPIN|EPT|ETL1|IB1099 | |
Cytomap | UCSC genome browser: 10q24 | |
Type of gene | protein-coding | |
RefGenes | NM_005097.2, | |
Description | epitempin-1leucine-rich glioma-inactivated protein 1 | |
Modification date | 20141219 | |
dbXrefs | MIM : 604619 | |
HGNC : HGNC | ||
Ensembl : ENSG00000108231 | ||
HPRD : 05216 | ||
Vega : OTTHUMG00000018777 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LGI1 | |
BioGPS: 9211 | ||
Pathway | NCI Pathway Interaction Database: LGI1 | |
KEGG: LGI1 | ||
REACTOME: LGI1 | ||
Pathway Commons: LGI1 | ||
Context | iHOP: LGI1 | |
ligand binding site mutation search in PubMed: LGI1 | ||
UCL Cancer Institute: LGI1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | HPA,TiGER | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Brain | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGG | |
Reference showing the relevant tissue of LGI1 | ||
Description by TissGene annotations | Cancer gene Have significant anti-correlated miRNA Fused withTSGene |
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C. |
Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez |
GO ID | GO term | PubMed ID |
Top |
TissGeneExp for LGI1 |
Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01) |
Gene expressions across normal tissues of GTEx data (GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct) - Here, we shows the matched tissue types only among our 28 cancer types. |
Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1)) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) |
- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05) |
Cancer type | Mean(exp) in tumor | Mean(exp) in matched normal | Log2FC | P-val. | FDR |
HNSC | -2.109966473 | 0.043412597 | -2.15337907 | 4.02E-10 | 7.18E-09 |
BRCA | -1.89997702 | -0.686104213 | -1.213872807 | 1.71E-10 | 6.61E-10 |
LIHC | -2.051022985 | -0.086392985 | -1.96463 | 6.75E-07 | 3.78E-06 |
THCA | -2.234472307 | -0.912716375 | -1.321755932 | 3.84E-13 | 3.71E-12 |
COAD | -2.015624523 | 2.488410092 | -4.504034615 | 5.79E-21 | 3.30E-18 |
BLCA | -2.321891932 | 0.727013331 | -3.048905263 | 1.21E-09 | 2.07E-07 |
STAD | -1.39392861 | 1.882330765 | -3.276259375 | 6.79E-12 | 1.70E-09 |
ESCA | -1.528558439 | 1.443641561 | -2.9722 | 0.000665 | 0.011037015 |
PRAD | -0.731955292 | 0.287821631 | -1.019776923 | 0.000875 | 0.00288364 |
Top |
TissGene-miRNA for LGI1 |
Significantly anti-correlated miRNAs of TissGene across 28 cancer types (Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016) (TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21) (TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16) (Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25)) |
Cancer type | miRNA id | miRNA accession | P-val. | Coeff. | # samples |
UCS | hsa-miR-34a-5p | MIMAT0000255 | 0.019 | -0.32 | 56 |
Top |
TissGeneMut for LGI1 |
TissGeneSNV for LGI1 |
nsSNV counts per each loci. Different colors of circles represent different cancer types. Circle size denotes number of samples. (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) * Click on the image to enlarge it in a new window. |
Somatic nucleotide variants of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of mutated samples) The numbers in parentheses are numbers of samples with mutation (nsSNVs). (TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25) |
- nsSNVs sorted by frequency. |
AAchange | Cancer type | # samples |
p.G475E | SKCM | 2 |
p.S216L | SKCM | 2 |
p.Q469H | LUAD | 1 |
p.D220N | SKCM | 1 |
p.L144F | LUAD | 1 |
p.N534T | UCEC | 1 |
p.Y502C | LIHC | 1 |
p.E516K | SKCM | 1 |
p.S497F | SKCM | 1 |
p.V251F | LUAD | 1 |
p.R5* | SKCM | 1 |
p.V75A | UCEC | 1 |
p.K513* | SKCM | 1 |
p.L23I | UCEC | 1 |
p.I468V | LGG | 1 |
p.W183C | LUAD | 1 |
p.S213I | LUAD | 1 |
p.G366E | SKCM | 1 |
p.R136L | ACC | 1 |
p.E248* | SKCM | 1 |
p.S476C | LUAD | 1 |
p.K459T | UCEC | 1 |
p.I308M | HNSC | 1 |
p.S352L | SKCM | 1 |
p.K339N | UCEC | 1 |
p.S529F | SKCM | 1 |
p.L492I | COAD | 1 |
p.S71L | ESCA | 1 |
p.A375T | BRCA | 1 |
p.G85E | COAD | 1 |
p.E507D | UCEC | 1 |
p.P43T | LUAD | 1 |
p.D431N | SKCM | 1 |
p.E196Q | BLCA | 1 |
p.R533H | UCEC | 1 |
p.R407H | LGG | 1 |
p.C48* | LUSC | 1 |
p.V65I | STAD | 1 |
p.R209H | COAD | 1 |
p.S215F | SKCM | 1 |
p.E264Q | OV | 1 |
p.R533H | READ | 1 |
p.L302P | LGG | 1 |
p.E430* | UCEC | 1 |
p.F338Y | LGG | 1 |
p.R311Q | UCEC | 1 |
p.R311* | STAD | 1 |
p.Q469H | CESC | 1 |
p.R474Q | COAD | 1 |
p.P62Q | UCEC | 1 |
p.S73C | BRCA | 1 |
p.E341K | SKCM | 1 |
p.E386X | COAD | 1 |
p.E248X | SKCM | 1 |
p.G461R | SKCM | 1 |
p.R311X | STAD | 1 |
p.V528M | BRCA | 1 |
p.P255H | UCEC | 1 |
p.I410T | PRAD | 1 |
p.T357I | STAD | 1 |
p.S92L | SKCM | 1 |
p.W362X | SKCM | 1 |
p.W504* | LUAD | 1 |
p.P391H | BLCA | 1 |
p.S464L | SKCM | 1 |
p.N428S | HNSC | 1 |
p.R209C | ESCA | 1 |
p.R378S | LUSC | 1 |
p.Q423H | LUAD | 1 |
p.S282F | SKCM | 1 |
p.E269K | SKCM | 1 |
p.L117V | BLCA | 1 |
p.E4Q | BLCA | 1 |
p.T358I | READ | 1 |
p.R59T | ESCA | 1 |
p.F87V | COAD | 1 |
p.W362* | SKCM | 1 |
p.N149I | UCEC | 1 |
p.S405F | SKCM | 1 |
p.P204R | OV | 1 |
Top |
TissGeneCNV for LGI1 |
Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples) (TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16) |
Top |
TissGeneFusions for LGI1 |
Fusion genes including TissGene (ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01) |
Database | Src | Cancer type | Sample | Fusion gene | ORF | 5'-gene BP | 3'-gene BP |
Chimerdb3.0 | FusionScan | ESCA | TCGA-L5-A4OQ-01A | PLCE1-LGI1 | In-Frame | chr10:95995877 | chr10:95537135 |
Top |
TissGeneNet for LGI1 |
Co-expressed gene networks based on protein-protein interaction data (CePIN) (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (PINA2 ppi data) |
Top |
TissGeneProg for LGI1 |
Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image to enlarge it in a new window. |
Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types (TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16) (TCGA clinicalMatrix, phenotype data, version 2016-04-27) * Click on the image enlarge it in a new window. |
Top |
TissGeneClin for LGI1 |
TissGeneDrug for LGI1 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
Top |
TissGeneDisease for LGI1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C1838062 | EPILEPSY, LATERAL TEMPORAL LOBE, AUTOSOMAL DOMINANT | 33 | BeFree,CLINVAR,CTD_human,MGD,UNIPROT |
umls:C0014544 | Epilepsy | 31 | BeFree,GAD,LHGDN |
umls:C0393682 | Epilepsy, Lateral Temporal | 17 | BeFree |
umls:C0017638 | Glioma | 14 | BeFree,CTD_human,LHGDN |
umls:C0014547 | Epilepsies, Partial | 12 | BeFree,GAD,LHGDN |
umls:C0014556 | Epilepsy, Temporal Lobe | 12 | BeFree,LHGDN |
umls:C0036572 | Seizures | 11 | BeFree |
umls:C0338430 | Limbic Encephalitis | 5 | BeFree |
umls:C0009952 | Febrile Convulsions | 4 | BeFree |
umls:C0017636 | Glioblastoma | 4 | BeFree |
umls:C0234461 | aphasic | 4 | BeFree |
umls:C1842564 | Temporal epilepsy, familial | 4 | BeFree |
umls:C0006118 | Brain Neoplasms | 3 | BeFree |
umls:C0027627 | Neoplasm Metastasis | 3 | BeFree |
umls:C0391957 | idiopathic epilepsy | 3 | BeFree |
umls:C0555198 | Malignant Glioma | 3 | BeFree |
umls:C0751495 | Seizures, Focal | 3 | BeFree |
umls:C0014548 | Epilepsy, Generalized | 2 | BeFree |
umls:C0027765 | nervous system disorder | 2 | BeFree,LHGDN |
umls:C1621958 | Glioblastoma Multiforme | 2 | BeFree |
umls:C0004114 | Astrocytoma | 1 | BeFree |
umls:C0004364 | Autoimmune Diseases | 1 | BeFree |
umls:C0011570 | Mental Depression | 1 | BeFree |
umls:C0011581 | Depressive disorder | 1 | BeFree |
umls:C0027626 | Neoplasm Invasiveness | 1 | LHGDN |
umls:C0027819 | Neuroblastoma | 1 | BeFree |
umls:C0085584 | Encephalopathies | 1 | BeFree |
umls:C0086132 | Depressive Symptoms | 1 | BeFree |
umls:C0234533 | Generalized seizures | 1 | BeFree |
umls:C0242287 | Isaacs syndrome | 1 | BeFree |
umls:C0242363 | Islet Cell Tumor | 1 | BeFree |
umls:C0270850 | Idiopathic generalized epilepsy | 1 | BeFree |
umls:C0279626 | Squamous cell carcinoma of esophagus | 1 | BeFree |
umls:C0334583 | Pilocytic Astrocytoma | 1 | BeFree |
umls:C0346957 | Disseminated Malignant Neoplasm | 1 | BeFree |
umls:C0422943 | Visual symptoms | 1 | BeFree |
umls:C0454578 | Receptive aphasia (finding) | 1 | BeFree |
umls:C0686619 | Secondary malignant neoplasm of lymph node | 1 | BeFree |
umls:C0700095 | Central neuroblastoma | 1 | BeFree |
umls:C0751919 | Acquired Neuromyotonia | 1 | BeFree |
umls:C1271104 | Blood pressure finding | 1 | GAD |
umls:C1272641 | Systemic arterial pressure | 1 | GAD |