TissGeneSummary for LCN1 |
Gene summary |
Basic gene information | Gene symbol | LCN1 |
Gene name | lipocalin 1 | |
Synonyms | PMFA|TLC|TP|VEGP | |
Cytomap | UCSC genome browser: 9q34 | |
Type of gene | protein-coding | |
RefGenes | NM_001252617.1, NM_001252618.1,NM_001252619.1,NM_002297.3, | |
Description | VEG proteinVon Ebner gland proteinlipocalin 1 (tear prealbumin)lipocalin-1protein migrating faster than albumintear prealbumin | |
Modification date | 20141207 | |
dbXrefs | MIM : 151675 | |
HGNC : HGNC | ||
Ensembl : ENSG00000160349 | ||
HPRD : 01059 | ||
Vega : OTTHUMG00000020908 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LCN1 | |
BioGPS: 3933 | ||
Pathway | NCI Pathway Interaction Database: LCN1 | |
KEGG: LCN1 | ||
REACTOME: LCN1 | ||
Pathway Commons: LCN1 | ||
Context | iHOP: LCN1 | |
ligand binding site mutation search in PubMed: LCN1 | ||
UCL Cancer Institute: LCN1 | ||
Assigned class in TissGDB* | C | |
Included tissue-specific gene expression resources | TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | EsophagusEye | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | ESCAUVM | |
Reference showing the relevant tissue of LCN1 | ||
Description by TissGene annotations | 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 |
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TissGeneExp for LCN1 |
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 |
PRAD | -2.489926932 | -1.452853855 | -1.037073077 | 0.00608 | 0.015483273 |
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TissGene-miRNA for LCN1 |
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 LCN1 |
TissGeneSNV for LCN1 |
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.R129Q | KIRP | 1 |
p.E146G | KIRC | 1 |
p.R129Q | LGG | 1 |
p.D176N | SKCM | 1 |
p.G77A | HNSC | 1 |
p.G93R | KIRC | 1 |
p.P173T | LUAD | 1 |
p.P127S | GBM | 1 |
p.N66Y | ESCA | 1 |
p.E120D | TGCT | 1 |
p.G173E | SKCM | 1 |
p.G125E | SKCM | 1 |
p.K70E | UCEC | 1 |
p.E87K | SKCM | 1 |
p.D176N | BLCA | 1 |
p.E146K | SKCM | 1 |
p.G93E | HNSC | 1 |
p.D90E | LUAD | 1 |
p.C171R | LUAD | 1 |
p.W144X | SKCM | 1 |
p.D25G | KIRC | 1 |
p.G125R | SKCM | 1 |
p.A97T | SKCM | 1 |
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TissGeneCNV for LCN1 |
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 LCN1 |
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 | CD723346 | LCN1-HECA | chr9:138416738 | chr6:139501807 | |
Chimerdb3.0 | ChiTaRs | NA | CK429413 | LCN1-LYZ | chr9:138414015 | chr12:69746005 | |
Chimerdb3.0 | ChiTaRs | NA | CK430284 | LCN1-LCN1 | chr9:138418082 | chr9:138417142 |
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TissGeneNet for LCN1 |
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 LCN1 |
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 LCN1 |
TissGeneDrug for LCN1 |
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 LCN1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0002395 | Alzheimer's Disease | 1 | GAD |
umls:C0006272 | Bronchiolitis Obliterans | 1 | BeFree |
umls:C0007138 | Carcinoma, Transitional Cell | 1 | BeFree |
umls:C0015230 | Exanthema | 1 | BeFree |
umls:C0026946 | Mycoses | 1 | BeFree |
umls:C0206664 | Teratocarcinoma | 1 | BeFree |
umls:C0278488 | Carcinoma breast stage IV | 1 | BeFree |
umls:C0677898 | invasive cancer | 1 | BeFree |
umls:C0848332 | Spots on skin | 1 | BeFree |
umls:C1527336 | Sjogren's Syndrome | 1 | LHGDN |