 |
| |
| |
| |
| |
| |
| |
|
| TissGeneSummary for LHX1 |
 Gene summary |
| Basic gene information | Gene symbol | LHX1 |
| Gene name | LIM homeobox 1 | |
| Synonyms | LIM-1|LIM1 | |
| Cytomap | UCSC genome browser: 17q12 | |
| Type of gene | protein-coding | |
| RefGenes | NM_005568.4, | |
| Description | LIM homeobox protein 1LIM/homeobox protein Lhx1homeobox protein Lim-1 | |
| Modification date | 20141207 | |
| dbXrefs | MIM : 601999 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000273706 | ||
| HPRD : 09067 | ||
| Vega : OTTHUMG00000188456 | ||
| Protein | UniProt: go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_LHX1 | |
| BioGPS: 3975 | ||
| Pathway | NCI Pathway Interaction Database: LHX1 | |
| KEGG: LHX1 | ||
| REACTOME: LHX1 | ||
| Pathway Commons: LHX1 | ||
| Context | iHOP: LHX1 | |
| ligand binding site mutation search in PubMed: LHX1 | ||
| UCL Cancer Institute: LHX1 | ||
| Assigned class in TissGDB* | A | |
| Included tissue-specific gene expression resources | HPA,TiGER,GTEx | |
| Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | KidneyOvary | |
| Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | KIRC,KIRP,KICHOV | |
| Reference showing the relevant tissue of LHX1 | Functional genetic targeting of embryonic kidney progenitor cells ex vivo. Junttila S, Saarela U, Halt K, Manninen A, Pärssinen H, Lecca MR, Brändli AW, Sims-Lucas S, Skovorodkin I, Vainio SJ. J Am Soc Nephrol. 2015 May;26(5):1126-37. doi: 10.1681/ASN.2013060584. Epub 2014 Sep 8. (pmid:25201883) go to article | |
| 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 |
| Top |
| TissGeneExp for LHX1 |
| 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 | -0.174279723 | -1.239099331 | 1.064819608 | 3.47E-05 | 7.51E-05 |
| KIRP | 0.874887005 | 6.09200888 | -5.217121875 | 3.98E-12 | 5.83E-11 |
| KICH | -0.01476137 | 5.69966263 | -5.714424 | 5.30E-10 | 3.53E-09 |
| KIRC | 0.483038741 | 5.803849852 | -5.320811111 | 1.04E-34 | 2.68E-33 |
| HNSC | 2.295309606 | -0.867481091 | 3.162790698 | 8.66E-12 | 2.34E-10 |
| LUAD | -0.035687025 | -1.220362888 | 1.184675862 | 0.000114 | 0.00028602 |
| Top |
| TissGene-miRNA for LHX1 |
| 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 |
| Top |
| TissGeneMut for LHX1 |
| TissGeneSNV for LHX1 |
| 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.R184C | STAD | 2 |
| p.D294N | UCEC | 1 |
| p.R253C | UCEC | 1 |
| p.Q68E | GBM | 1 |
| p.G101C | KIRP | 1 |
| p.S380P | LIHC | 1 |
| p.T135P | KIRP | 1 |
| p.A153T | PAAD | 1 |
| p.N87H | KIRC | 1 |
| p.G6D | LGG | 1 |
| p.A197V | PAAD | 1 |
| p.A166V | COAD | 1 |
| p.S338R | LUAD | 1 |
| p.R14S | PRAD | 1 |
| p.R257Q | STAD | 1 |
| p.E358K | BLCA | 1 |
| p.T322M | STAD | 1 |
| p.S156L | COAD | 1 |
| p.Q304X | COAD | 1 |
| p.Q304* | UCEC | 1 |
| p.Q174K | PCPG | 1 |
| p.E371K | BLCA | 1 |
| p.E402K | UCEC | 1 |
| p.E399K | UCEC | 1 |
| p.S44C | BLCA | 1 |
| p.A153T | COAD | 1 |
| p.L119R | SARC | 1 |
| p.P336T | LUAD | 1 |
| p.F89L | READ | 1 |
| p.R236W | HNSC | 1 |
| p.T194M | BLCA | 1 |
| p.R80W | UCEC | 1 |
| p.G245S | UCEC | 1 |
| p.C66W | HNSC | 1 |
| p.R181W | LIHC | 1 |
| p.G386S | COAD | 1 |
| p.M1I | SKCM | 1 |
| p.H25Y | SKCM | 1 |
| p.K82I | PRAD | 1 |
| p.Q306* | SKCM | 1 |
| p.R181Q | ACC | 1 |
| p.A388E | LUAD | 1 |
| p.M238I | BLCA | 1 |
| p.W227G | ESCA | 1 |
| p.R181Q | LGG | 1 |
| p.G352R | STAD | 1 |
| Top |
| TissGeneCNV for LHX1 |
| 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 LHX1 |
| 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 |
| Top |
| TissGeneNet for LHX1 |
| 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) |
| BRCA (tumor) | BRCA (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| COAD (tumor) | COAD (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| HNSC (tumor) | HNSC (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| KICH (tumor) | KICH (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| KIRC (tumor) | KIRC (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| KIRP (tumor) | KIRP (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| LIHC (tumor) | LIHC (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| LUAD (tumor) | LUAD (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| LUSC (tumor) | LUSC (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| PRAD (tumor) | PRAD (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| STAD (tumor) | STAD (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| THCA (tumor) | THCA (normal) |
| LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (tumor) | LHX1, RLIM, ISL1, OTX2, LHX3, FOXA2 (normal) |
 |  |
| Top |
| TissGeneProg for LHX1 |
| 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 LHX1 |
| TissGeneDrug for LHX1 |
| 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 LHX1 |
| Disease information associated with TissGene (DisGeNet, 2016-06-01) |
| Disease ID | Disease name | # pubmeds | Source |
| umls:C0007134 | Renal Cell Carcinoma | 2 | BeFree |
| umls:C0431637 | Mullerian aplasia | 2 | BeFree |
| umls:C1698581 | Rokitansky Kuster Hauser syndrome | 2 | BeFree |
| umls:C0000768 | Congenital Abnormality | 1 | BeFree |
| umls:C0243050 | Cardiovascular Abnormalities | 1 | BeFree |
| umls:C0596263 | Carcinogenesis | 1 | BeFree |
| umls:C1705254 | Neonatal Deformity | 1 | BeFree |
| umls:C1720887 | Female Urogenital Diseases | 1 | CTD_human |
| umls:C3281138 | CHROMOSOME 17q12 DELETION SYNDROME | 0 | ORPHANET |
Copyright 2016-Present - The University of Texas Health Science Center at Houston (UTHealth) Web File Viewing | How to Report, Fraud, Waste and Abuse | State of Texas | Statewide Search | Texas Homeland Security | Site Policies |