TissGeneSummary for LCA5L |
Gene summary |
Basic gene information | Gene symbol | LCA5L |
Gene name | Leber congenital amaurosis 5-like | |
Synonyms | C21orf13 | |
Cytomap | UCSC genome browser: 21q22.2 | |
Type of gene | protein-coding | |
RefGenes | NM_152505.3, | |
Description | Lebercilin-like proteinleber congenital amaurosis 5-like protein | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000157578 | ||
HPRD : 10742 | ||
Vega : OTTHUMG00000066280 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LCA5L | |
BioGPS: 150082 | ||
Pathway | NCI Pathway Interaction Database: LCA5L | |
KEGG: LCA5L | ||
REACTOME: LCA5L | ||
Pathway Commons: LCA5L | ||
Context | iHOP: LCA5L | |
ligand binding site mutation search in PubMed: LCA5L | ||
UCL Cancer Institute: LCA5L | ||
Assigned class in TissGDB* | B | |
Included tissue-specific gene expression resources | HPA,TiGER,GTEx | |
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx) | Testis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
Reference showing the relevant tissue of LCA5L | ||
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 LCA5L |
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 |
KICH | -1.724756446 | 0.428163554 | -2.15292 | 2.06E-12 | 2.29E-11 |
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TissGene-miRNA for LCA5L |
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 LCA5L |
TissGeneSNV for LCA5L |
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.E465X | READ | 1 |
p.H643N | ESCA | 1 |
p.K47N | BLCA | 1 |
p.S380P | LIHC | 1 |
p.D240N | SKCM | 1 |
p.E456K | SKCM | 1 |
p.R340X | READ | 1 |
p.Q173* | SKCM | 1 |
p.R82I | UCEC | 1 |
p.F15L | READ | 1 |
p.Q638* | CESC | 1 |
p.S648C | BLCA | 1 |
p.R142P | HNSC | 1 |
p.T403N | SKCM | 1 |
p.E111D | SARC | 1 |
p.E491* | UCEC | 1 |
p.S659L | OV | 1 |
p.E433K | HNSC | 1 |
p.G573R | SKCM | 1 |
p.A28T | LIHC | 1 |
p.P410L | COAD | 1 |
p.D272G | SKCM | 1 |
p.L196I | READ | 1 |
p.E219K | SKCM | 1 |
p.K30N | LUAD | 1 |
p.R301Q | TGCT | 1 |
p.V18M | DLBC | 1 |
p.E332Q | BRCA | 1 |
p.Q212* | BRCA | 1 |
p.D350E | ESCA | 1 |
p.R142* | UCEC | 1 |
p.A544V | COAD | 1 |
p.Q105* | UCEC | 1 |
p.T514M | READ | 1 |
p.G446R | BLCA | 1 |
p.R40W | ESCA | 1 |
p.R340* | UCEC | 1 |
p.R424I | COAD | 1 |
p.V207I | LUAD | 1 |
p.F15L | STAD | 1 |
p.S101Y | UCEC | 1 |
p.R562T | LUAD | 1 |
p.L144P | LGG | 1 |
p.E563K | HNSC | 1 |
p.Q307E | BRCA | 1 |
p.E601* | UCEC | 1 |
p.E408* | UCEC | 1 |
p.I266S | UCEC | 1 |
p.I199L | COAD | 1 |
p.S614* | CESC | 1 |
p.P88L | SKCM | 1 |
p.N195S | KIRC | 1 |
p.G17S | COAD | 1 |
p.S631L | UCEC | 1 |
p.D503N | SKCM | 1 |
p.L235S | BLCA | 1 |
p.L183F | CESC | 1 |
p.E349K | SKCM | 1 |
p.E474D | STAD | 1 |
p.S2Y | UCEC | 1 |
p.D272Y | BRCA | 1 |
p.R340Q | SKCM | 1 |
p.V89A | LGG | 1 |
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TissGeneCNV for LCA5L |
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 LCA5L |
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 |
TCGAfusionPortal | PRADA | BRCA | TCGA-A8-A08P-01A | BRWD1-LCA5L | CDS-5UTR | Chr21:40585407 | Chr21:40801137 |
TCGAfusionPortal | PRADA | LUAD | TCGA-05-4397-01A | PDXK-LCA5L | CDS-5UTR | Chr21:45168961 | Chr21:40801137 |
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TissGeneNet for LCA5L |
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 LCA5L |
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 LCA5L |
TissGeneDrug for LCA5L |
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 LCA5L |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0013080 | Down Syndrome | 1 | CTD_human |
umls:C0151786 | Muscle Weakness | 1 | CTD_human |