TissGeneSummary for TM4SF4 |
Gene summary |
Basic gene information | Gene symbol | TM4SF4 |
Gene name | transmembrane 4 L six family member 4 | |
Synonyms | ILTMP|il-TMP | |
Cytomap | UCSC genome browser: 3q25 | |
Type of gene | protein-coding | |
RefGenes | NM_004617.3, | |
Description | intestinal and liver (il) tetraspan membrane proteinintestine and liver tetraspan membrane proteintransmembrane 4 L6 family member 4transmembrane 4 superfamily member 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 606567 | |
HGNC : HGNC | ||
HPRD : 07585 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_TM4SF4 | |
BioGPS: 7104 | ||
Pathway | NCI Pathway Interaction Database: TM4SF4 | |
KEGG: TM4SF4 | ||
REACTOME: TM4SF4 | ||
Pathway Commons: TM4SF4 | ||
Context | iHOP: TM4SF4 | |
ligand binding site mutation search in PubMed: TM4SF4 | ||
UCL Cancer Institute: TM4SF4 | ||
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) | LiverPancreas | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | LIHCPAAD | |
Reference showing the relevant tissue of TM4SF4 | ||
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 TM4SF4 |
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 | 0.767070314 | -1.867392398 | 2.634462712 | 5.62E-10 | 3.38E-09 |
KICH | -3.492082093 | -0.634634093 | -2.857448 | 6.81E-08 | 3.21E-07 |
LUSC | -2.783309779 | -0.595068603 | -2.188241176 | 4.39E-13 | 2.12E-12 |
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TissGene-miRNA for TM4SF4 |
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 TM4SF4 |
TissGeneSNV for TM4SF4 |
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.D199H | BLCA | 2 |
p.G104* | LUAD | 1 |
p.G102E | HNSC | 1 |
p.G50R | KICH | 1 |
p.G79S | SARC | 1 |
p.M171K | COAD | 1 |
p.R86Q | SKCM | 1 |
p.D139G | STAD | 1 |
p.G56S | KIRC | 1 |
p.D139Y | LUSC | 1 |
p.V178L | THYM | 1 |
p.D139Y | CHOL | 1 |
p.N25S | SKCM | 1 |
p.V166A | COAD | 1 |
p.S43F | SKCM | 1 |
p.I169V | SKCM | 1 |
p.R147Q | LUSC | 1 |
p.C75* | SARC | 1 |
p.S113L | BLCA | 1 |
p.R86Q | UCEC | 1 |
p.S106L | SKCM | 1 |
p.I60V | OV | 1 |
p.Y129C | UCEC | 1 |
p.C74R | SKCM | 1 |
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TissGeneCNV for TM4SF4 |
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 TM4SF4 |
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-A7-A26G-01A | RNF13-TM4SF4 | 5UTR-CDS | Chr3:149531140 | Chr3:149216509 |
TCGAfusionPortal | PRADA | OV | TCGA-13-1495-01A | RNF13-TM4SF4 | 5UTR-CDS | Chr3:149531140 | Chr3:149193610 |
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TissGeneNet for TM4SF4 |
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 TM4SF4 |
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 TM4SF4 |
TissGeneDrug for TM4SF4 |
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 TM4SF4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0279000 | Liver and Intrahepatic Biliary Tract Carcinoma | 2 | BeFree |
umls:C0345904 | Malignant neoplasm of liver | 2 | BeFree |
umls:C2239176 | Liver carcinoma | 2 | BeFree |
umls:C0023895 | Liver diseases | 1 | CTD_human |
umls:C0029928 | Ovarian Diseases | 1 | BeFree |
umls:C0032460 | Polycystic Ovary Syndrome | 1 | LHGDN |
umls:C0152013 | Adenocarcinoma of lung (disorder) | 1 | BeFree |
umls:C0684249 | Carcinoma of lung | 1 | BeFree |