TissGeneSummary for LHX2 |
Gene summary |
Basic gene information | Gene symbol | LHX2 |
Gene name | LIM homeobox 2 | |
Synonyms | LH2|hLhx2 | |
Cytomap | UCSC genome browser: 9q33.3 | |
Type of gene | protein-coding | |
RefGenes | NM_004789.3, | |
Description | LIM HOX gene 2LIM homeobox protein 2LIM/homeobox protein Lhx2homeobox protein LH-2 | |
Modification date | 20141207 | |
dbXrefs | MIM : 603759 | |
HGNC : HGNC | ||
Ensembl : ENSG00000106689 | ||
HPRD : 04786 | ||
Vega : OTTHUMG00000020647 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LHX2 | |
BioGPS: 9355 | ||
Pathway | NCI Pathway Interaction Database: LHX2 | |
KEGG: LHX2 | ||
REACTOME: LHX2 | ||
Pathway Commons: LHX2 | ||
Context | iHOP: LHX2 | |
ligand binding site mutation search in PubMed: LHX2 | ||
UCL Cancer Institute: LHX2 | ||
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) | BrainEye | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | GBM,LGGUVM | |
Reference showing the relevant tissue of LHX2 | ||
Description by TissGene annotations |
* 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 |
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TissGeneExp for LHX2 |
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 |
LUSC | 0.339671843 | -3.801708549 | 4.141380392 | 5.87E-16 | 4.14E-15 |
LIHC | -0.701726196 | 1.865247804 | -2.566974 | 7.85E-14 | 2.00E-12 |
LUAD | -1.921845161 | -3.930884817 | 2.009039655 | 2.10E-11 | 1.39E-10 |
HNSC | 0.195636595 | -2.746814568 | 2.942451163 | 6.34E-11 | 1.35E-09 |
BRCA | -1.92611567 | -3.719562161 | 1.793446491 | 1.35E-20 | 1.01E-19 |
STAD | -2.330663696 | -3.369710571 | 1.039046875 | 0.000516 | 0.003102898 |
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TissGene-miRNA for LHX2 |
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 |
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TissGeneMut for LHX2 |
TissGeneSNV for LHX2 |
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.R130C | STAD | 2 |
p.D185Y | LUAD | 1 |
p.D34N | BLCA | 1 |
p.M158I | SKCM | 1 |
p.P360L | SKCM | 1 |
p.A171V | STAD | 1 |
p.R270H | STAD | 1 |
p.R132Q | COAD | 1 |
p.T379A | STAD | 1 |
p.Q311K | LIHC | 1 |
p.T391I | GBM | 1 |
p.T363M | PRAD | 1 |
p.G356V | LUSC | 1 |
p.P43S | PAAD | 1 |
p.A189V | COAD | 1 |
p.R270C | STAD | 1 |
p.R117H | STAD | 1 |
p.E25K | UCEC | 1 |
p.R270H | UCEC | 1 |
p.D70G | STAD | 1 |
p.P397S | SKCM | 1 |
p.Q315* | SKCM | 1 |
p.S357W | BRCA | 1 |
p.H155Y | SKCM | 1 |
p.A206V | SARC | 1 |
p.A348T | LUSC | 1 |
p.R138C | STAD | 1 |
p.G304C | KIRC | 1 |
p.P397L | SKCM | 1 |
p.S357L | BLCA | 1 |
p.S347W | BLCA | 1 |
p.T374I | BLCA | 1 |
p.I29T | LIHC | 1 |
p.Y213* | LUAD | 1 |
p.K335M | STAD | 1 |
p.S384Y | UCEC | 1 |
p.E248K | SKCM | 1 |
p.R268H | UCEC | 1 |
p.R270H | PRAD | 1 |
p.A189V | HNSC | 1 |
p.H276Y | SKCM | 1 |
p.A68V | SARC | 1 |
p.G58D | COAD | 1 |
p.R323C | STAD | 1 |
p.X407Q | LIHC | 1 |
p.A179T | UCEC | 1 |
p.A191T | STAD | 1 |
p.R256H | COAD | 1 |
p.L167F | OV | 1 |
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TissGeneCNV for LHX2 |
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) |
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TissGeneFusions for LHX2 |
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 | ChiTaRs | NA | BF953191 | LHX2-NR2F1 | chr9:126795222 | chr5:92929455 |
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TissGeneNet for LHX2 |
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) |
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TissGeneProg for LHX2 |
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. |
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TissGeneClin for LHX2 |
TissGeneDrug for LHX2 |
Drug information targeting TissGene (DrugBank Version 5.0.6, 2017-04-01) |
DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
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TissGeneDisease for LHX2 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0002871 | Anemia | 1 | BeFree |
umls:C0003119 | Anophthalmos | 1 | BeFree,GAD |
umls:C0003873 | Rheumatoid Arthritis | 1 | CTD_human |
umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
umls:C0021670 | insulinoma | 1 | BeFree |
umls:C0023473 | Myeloid Leukemia, Chronic | 1 | BeFree |
umls:C0023890 | Liver Cirrhosis | 1 | BeFree |
umls:C0026010 | Microphthalmos | 1 | GAD |
umls:C0027627 | Neoplasm Metastasis | 1 | BeFree |
umls:C0029408 | Degenerative polyarthritis | 1 | BeFree |
umls:C0032002 | Pituitary Diseases | 1 | BeFree |
umls:C0178874 | Tumor Progression | 1 | BeFree |
umls:C0239946 | Fibrosis, Liver | 1 | BeFree |
umls:C0596263 | Carcinogenesis | 1 | BeFree |
umls:C0678222 | Breast Carcinoma | 1 | BeFree |
umls:C1623038 | Cirrhosis | 1 | BeFree |