TissGeneSummary for TMEM56 |
Gene summary |
Basic gene information | Gene symbol | TMEM56 |
Gene name | transmembrane protein 56 | |
Synonyms | - | |
Cytomap | UCSC genome browser: 1p21.3 | |
Type of gene | protein-coding | |
RefGenes | NM_001199679.1, NM_152487.2, | |
Description | - | |
Modification date | 20141207 | |
dbXrefs | HGNC : HGNC | |
Ensembl : ENSG00000152078 | ||
HPRD : 08110 | ||
Vega : OTTHUMG00000010847 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TMEM56 | |
BioGPS: 148534 | ||
Pathway | NCI Pathway Interaction Database: TMEM56 | |
KEGG: TMEM56 | ||
REACTOME: TMEM56 | ||
Pathway Commons: TMEM56 | ||
Context | iHOP: TMEM56 | |
ligand binding site mutation search in PubMed: TMEM56 | ||
UCL Cancer Institute: TMEM56 | ||
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) | CervixLiver | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | CESCLIHC | |
Reference showing the relevant tissue of TMEM56 | ||
Description by TissGene annotations | Have significant anti-correlated miRNA |
* 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 TMEM56 |
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 | -1.323153413 | 0.258497567 | -1.58165098 | 2.07E-10 | 7.56E-10 |
LIHC | 3.140240744 | 4.534276744 | -1.394036 | 3.87E-11 | 5.37E-10 |
KIRC | -0.276816812 | 1.00550541 | -1.282322222 | 8.29E-18 | 5.34E-17 |
COAD | 0.700919513 | 2.094300282 | -1.393380769 | 9.91E-06 | 4.55E-05 |
BLCA | -0.781640204 | 0.46074927 | -1.242389474 | 0.00536 | 0.02778704 |
HNSC | -2.894349628 | -1.195458931 | -1.698890698 | 7.64E-05 | 0.000352977 |
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TissGene-miRNA for TMEM56 |
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 |
LUAD | hsa-miR-141-3p | MIMAT0000432 | 0.0024 | -0.39 | 60 |
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TissGeneMut for TMEM56 |
TissGeneSNV for TMEM56 |
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.W82L | KIRC | 1 |
p.D227N | SKCM | 1 |
p.M192I | SARC | 1 |
p.I245T | COAD | 1 |
p.K77E | LUAD | 1 |
p.G197V | HNSC | 1 |
p.L22F | SKCM | 1 |
p.K116N | PRAD | 1 |
p.Q157X | STAD | 1 |
p.G240C | UCEC | 1 |
p.V187M | COAD | 1 |
p.S27N | UCEC | 1 |
p.Y28H | SKCM | 1 |
p.F23L | STAD | 1 |
p.K236T | READ | 1 |
p.Y203H | UCS | 1 |
p.V11A | LGG | 1 |
p.V90M | LUAD | 1 |
p.G97D | COAD | 1 |
p.T5R | BLCA | 1 |
p.A172T | SKCM | 1 |
p.I242M | BLCA | 1 |
p.V174I | STAD | 1 |
p.Q157* | STAD | 1 |
p.R145C | LUAD | 1 |
p.F23L | LIHC | 1 |
p.E162G | THYM | 1 |
p.V202M | THYM | 1 |
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TissGeneCNV for TMEM56 |
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 TMEM56 |
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 | AW362912 | ZCCHC10-TMEM56 | chr5:132339336 | chr1:95576560 | |
Chimerdb3.0 | ChiTaRs | NA | BF306134 | TMEM56-DDOST | chr1:95639966 | chr1:20978617 | |
TCGAfusionPortal | PRADA | BRCA | TCGA-A8-A07L-01A | RWDD3-TMEM56 | Out-of-frame | Chr1:95699871 | Chr1:95639372 |
TCGAfusionPortal | PRADA | BRCA | TCGA-D8-A1X5-01A | TMEM56-FNBP1L | Out-of-frame | Chr1:95639445 | Chr1:93965025 |
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TissGeneNet for TMEM56 |
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 TMEM56 |
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 TMEM56 |
TissGeneDrug for TMEM56 |
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 TMEM56 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0040336 | Tobacco Use Disorder | 1 | GAD |
umls:C0400966 | Non-alcoholic Fatty Liver Disease | 1 | GAD |