TissGeneSummary for SMC4 |
Gene summary |
Basic gene information | Gene symbol | SMC4 |
Gene name | structural maintenance of chromosomes 4 | |
Synonyms | CAP-C|CAPC|SMC-4|SMC4L1|hCAP-C | |
Cytomap | UCSC genome browser: 3q26.1 | |
Type of gene | protein-coding | |
RefGenes | NM_001002799.1, NM_001002800.2,NM_001288753.1,NM_005496.3, | |
Description | SMC protein 4SMC4 structural maintenance of chromosomes 4-like 1XCAP-C homologchromosome-associated polypeptide Cstructural maintenance of chromosomes protein 4 | |
Modification date | 20141207 | |
dbXrefs | MIM : 605575 | |
HGNC : HGNC | ||
Ensembl : ENSG00000113810 | ||
HPRD : 09276 | ||
Vega : OTTHUMG00000159006 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_SMC4 | |
BioGPS: 10051 | ||
Pathway | NCI Pathway Interaction Database: SMC4 | |
KEGG: SMC4 | ||
REACTOME: SMC4 | ||
Pathway Commons: SMC4 | ||
Context | iHOP: SMC4 | |
ligand binding site mutation search in PubMed: SMC4 | ||
UCL Cancer Institute: SMC4 | ||
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) | BladderTestis | |
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA) | BLCATGCT | |
Reference showing the relevant tissue of SMC4 | ||
Description by TissGene annotations | TissgsLTS |
* 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 | GO:0007076 | mitotic chromosome condensation | 11136719 | GO:0007076 | mitotic chromosome condensation | 11136719 |
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TissGeneExp for SMC4 |
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 |
LIHC | 1.132291956 | 0.047743956 | 1.084548 | 4.36E-10 | 5.09E-09 |
LUSC | 3.084539643 | 1.496169054 | 1.588370588 | 2.41E-21 | 3.41E-20 |
BRCA | 2.42730729 | 0.987697641 | 1.439609649 | 9.83E-41 | 3.17E-39 |
HNSC | 2.777091398 | 1.652177445 | 1.124913953 | 8.69E-09 | 1.08E-07 |
ESCA | 3.038769411 | 1.922914865 | 1.115854545 | 0.00058 | 0.010120062 |
BLCA | 2.545666062 | 1.175260798 | 1.370405263 | 1.47E-05 | 0.000259467 |
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TissGene-miRNA for SMC4 |
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 SMC4 |
TissGeneSNV for SMC4 |
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.R1252* | UCEC | 5 |
p.D1126H | BLCA | 2 |
p.Y1096C | ESCA | 2 |
p.R1252X | COAD | 1 |
p.F1235L | UCEC | 1 |
p.E996D | HNSC | 1 |
p.A1065V | UCEC | 1 |
p.R660G | LUAD | 1 |
p.S1231A | BLCA | 1 |
p.N1270T | STAD | 1 |
p.F1205V | STAD | 1 |
p.E1019Q | ACC | 1 |
p.Q399K | PAAD | 1 |
p.S117C | LUAD | 1 |
p.L807V | UCEC | 1 |
p.E314K | LUAD | 1 |
p.Q730E | CESC | 1 |
p.E1101* | LUSC | 1 |
p.R991C | BLCA | 1 |
p.N377D | STAD | 1 |
p.P8L | LUSC | 1 |
p.R827H | STAD | 1 |
p.R991H | LGG | 1 |
p.P549A | SKCM | 1 |
p.L807S | COAD | 1 |
p.D1226H | CESC | 1 |
p.E1085K | LUAD | 1 |
p.E450X | LIHC | 1 |
p.I927N | LUSC | 1 |
p.A678V | UCEC | 1 |
p.A865V | UCEC | 1 |
p.S609T | LGG | 1 |
p.S491L | SARC | 1 |
p.M499I | HNSC | 1 |
p.R214* | SKCM | 1 |
p.E552Q | ESCA | 1 |
p.L127I | UCS | 1 |
p.D701Y | OV | 1 |
p.D630H | BLCA | 1 |
p.R713L | LUSC | 1 |
p.S531C | LUAD | 1 |
p.S117C | UCEC | 1 |
p.E833K | BLCA | 1 |
p.P1169S | SKCM | 1 |
p.P549S | SARC | 1 |
p.A675D | STAD | 1 |
p.K416N | STAD | 1 |
p.L1018I | UCEC | 1 |
p.D956N | LUAD | 1 |
p.K153M | OV | 1 |
p.R214Q | BRCA | 1 |
p.K136I | READ | 1 |
p.D174A | LGG | 1 |
p.D904N | CESC | 1 |
p.K420N | STAD | 1 |
p.Q581* | BLCA | 1 |
p.W677C | PRAD | 1 |
p.D601G | STAD | 1 |
p.I909R | BRCA | 1 |
p.E770G | SKCM | 1 |
p.I123T | LUAD | 1 |
p.S143T | UCEC | 1 |
p.S215G | STAD | 1 |
p.S1177G | STAD | 1 |
p.E1061D | LGG | 1 |
p.K422R | COAD | 1 |
p.D1158N | HNSC | 1 |
p.R692C | UCEC | 1 |
p.A872D | UCEC | 1 |
p.D904H | BLCA | 1 |
p.G1156R | SKCM | 1 |
p.N992D | SARC | 1 |
p.T521A | STAD | 1 |
p.Q392* | UCEC | 1 |
p.K573E | BLCA | 1 |
p.A678V | READ | 1 |
p.S1231F | UCS | 1 |
p.S589L | LUAD | 1 |
p.S491L | UCEC | 1 |
p.S1259L | UCEC | 1 |
p.M681I | BLCA | 1 |
p.E801K | CESC | 1 |
p.F668S | SKCM | 1 |
p.Q903L | LUAD | 1 |
p.E811K | UCEC | 1 |
p.K365N | CESC | 1 |
p.R705C | READ | 1 |
p.E98G | COAD | 1 |
p.V758L | LGG | 1 |
p.R272Q | LUAD | 1 |
p.H216Y | SKCM | 1 |
p.A1026T | ESCA | 1 |
p.R726G | UCEC | 1 |
p.K106E | STAD | 1 |
p.V776I | COAD | 1 |
p.E1085K | CESC | 1 |
p.D174N | BLCA | 1 |
p.L565H | LUAD | 1 |
p.A305T | LUAD | 1 |
p.E1004K | THYM | 1 |
p.D601H | UCS | 1 |
p.A1094T | HNSC | 1 |
p.N720K | HNSC | 1 |
p.P851T | PRAD | 1 |
p.I1052S | UCEC | 1 |
p.E60K | BLCA | 1 |
p.F183V | UCEC | 1 |
p.E971K | STAD | 1 |
p.V162F | HNSC | 1 |
p.R512C | COAD | 1 |
p.E301K | DLBC | 1 |
p.L887F | LUAD | 1 |
p.D54H | BRCA | 1 |
p.D695H | BRCA | 1 |
p.G102E | SKCM | 1 |
p.E450* | LIHC | 1 |
p.R692H | UCEC | 1 |
p.R618I | HNSC | 1 |
p.E1220K | LUAD | 1 |
p.L835F | BLCA | 1 |
p.D150N | OV | 1 |
p.L721V | LIHC | 1 |
p.R827C | UCEC | 1 |
p.L228V | STAD | 1 |
p.C110S | UCEC | 1 |
p.I986M | ACC | 1 |
p.S143* | HNSC | 1 |
p.D397H | LUSC | 1 |
p.P1051H | PAAD | 1 |
p.E954K | LUAD | 1 |
p.D1010H | BLCA | 1 |
p.S109F | SKCM | 1 |
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TissGeneCNV for SMC4 |
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 SMC4 |
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 | FusionScan | ESCA | TCGA-2H-A9GN-01A | IFT80-SMC4 | Out-of-Frame | chr3:160093599 | chr3:160141212 |
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TissGeneNet for SMC4 |
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 SMC4 |
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 SMC4 |
TissGeneDrug for SMC4 |
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 SMC4 |
Disease information associated with TissGene (DisGeNet, 2016-06-01) |
Disease ID | Disease name | # pubmeds | Source |
umls:C0596263 | Carcinogenesis | 3 | BeFree |
umls:C0009402 | Colorectal Carcinoma | 2 | BeFree |
umls:C1527249 | Colorectal Cancer | 2 | BeFree |
umls:C2239176 | Liver carcinoma | 2 | BeFree |
umls:C0006142 | Malignant neoplasm of breast | 1 | BeFree |
umls:C0014013 | Empyema, Pleural | 1 | BeFree |
umls:C0017638 | Glioma | 1 | BeFree |
umls:C0017661 | IGA Glomerulonephritis | 1 | CTD_human |
umls:C0024299 | Lymphoma | 1 | BeFree,LHGDN |
umls:C0027627 | Neoplasm Metastasis | 1 | BeFree |
umls:C0376358 | Malignant neoplasm of prostate | 1 | BeFree |
umls:C0600139 | Prostate carcinoma | 1 | BeFree |
umls:C0678222 | Breast Carcinoma | 1 | BeFree |
umls:C1709781 | Pyothorax-Associated Lymphoma | 1 | BeFree |
umls:C1961099 | Precursor T-Cell Lymphoblastic Leukemia-Lymphoma | 1 | BeFree |