TissGeneSummary for LEMD1 |
Gene summary |
Basic gene information | Gene symbol | LEMD1 |
Gene name | LEM domain containing 1 | |
Synonyms | CT50|LEMP-1 | |
Cytomap | UCSC genome browser: 1q32.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001001552.4, NM_001199050.1,NM_001199051.1,NM_001199052.1,NR_037583.1, | |
Description | LEM domain protein 1LEM domain-containing protein 1cancer/testis antigen 50 | |
Modification date | 20141207 | |
dbXrefs | MIM : 610480 | |
HGNC : HGNC | ||
Ensembl : ENSG00000186007 | ||
HPRD : 13983 | ||
Vega : OTTHUMG00000037201 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_LEMD1 | |
BioGPS: 93273 | ||
Pathway | NCI Pathway Interaction Database: LEMD1 | |
KEGG: LEMD1 | ||
REACTOME: LEMD1 | ||
Pathway Commons: LEMD1 | ||
Context | iHOP: LEMD1 | |
ligand binding site mutation search in PubMed: LEMD1 | ||
UCL Cancer Institute: LEMD1 | ||
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) | Testis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | TGCT | |
Reference showing the relevant tissue of LEMD1 | ||
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 LEMD1 |
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 |
THCA | 3.651122495 | 0.999568258 | 2.651554237 | 3.87E-17 | 7.39E-16 |
KIRP | 1.181186213 | -1.120663787 | 2.30185 | 9.40E-06 | 3.95E-05 |
LUAD | 2.360964985 | 0.306296019 | 2.054668966 | 5.82E-09 | 2.69E-08 |
LUSC | 1.954693382 | 0.202671814 | 1.752021569 | 8.52E-07 | 2.15E-06 |
COAD | 1.773277319 | -2.065041912 | 3.838319231 | 1.47E-10 | 1.99E-09 |
STAD | 1.325270588 | -1.129229412 | 2.4545 | 1.19E-06 | 1.88E-05 |
KICH | -2.147753912 | -0.535113912 | -1.61264 | 3.88E-07 | 1.57E-06 |
BLCA | -0.192757701 | -1.700620859 | 1.507863158 | 0.00482 | 0.025768462 |
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TissGene-miRNA for LEMD1 |
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 LEMD1 |
TissGeneSNV for LEMD1 |
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.W147C | BLCA | 1 |
p.G151D | SKCM | 1 |
p.Q28X | STAD | 1 |
p.I144T | PAAD | 1 |
p.P46L | SKCM | 1 |
p.T173N | KIRC | 1 |
p.R92Q | UCEC | 1 |
p.E73* | ACC | 1 |
p.Q15L | SKCM | 1 |
p.E17Q | BLCA | 1 |
p.E145K | LUAD | 1 |
p.E134* | UCEC | 1 |
p.A91V | STAD | 1 |
p.W50G | COAD | 1 |
p.A80T | COAD | 1 |
p.G129R | SKCM | 1 |
p.T124I | THCA | 1 |
p.E145K | SKCM | 1 |
p.K11I | SKCM | 1 |
p.G110D | SKCM | 1 |
p.A48T | PRAD | 1 |
p.Q40K | STAD | 1 |
p.I26V | LUAD | 1 |
p.K37R | STAD | 1 |
p.S105F | SKCM | 1 |
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TissGeneCNV for LEMD1 |
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 LEMD1 |
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 | TopHat-Fusion | HNSC | TCGA-BA-6871-01A | NUAK2-LEMD1 | CDS-5'UTR | chr1:205280832 | chr1:205389701 |
TCGAfusionPortal | PRADA | HNSC | TCGA-BA-6871-01A | NUAK2-LEMD1 | CDS-5UTR | Chr1:205280833 | Chr1:205389702 |
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TissGeneNet for LEMD1 |
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 LEMD1 |
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 LEMD1 |
TissGeneDrug for LEMD1 |
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 LEMD1 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0009404 | Colorectal Neoplasms | 1 | LHGDN |