Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for SMG8
Basic gene info.Gene symbolSMG8
Gene nameSMG8 nonsense mediated mRNA decay factor
SynonymsC17orf71
CytomapUCSC genome browser: 17q22
Genomic locationchr17 :57287370-57292611
Type of geneprotein-coding
RefGenesNM_018149.6,
Ensembl idENSG00000167447
Descriptionamplified in breast cancer gene 2 proteinprotein SMG8protein smg-8 homologsmg-8 homolog, nonsense mediated mRNA decay factor
Modification date20141207
dbXrefs MIM : 613175
HGNC : HGNC
Ensembl : ENSG00000167447
HPRD : 08551
Vega : OTTHUMG00000179365
ProteinUniProt: Q8ND04
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMG8
BioGPS: 55181
Gene Expression Atlas: ENSG00000167447
The Human Protein Atlas: ENSG00000167447
PathwayNCI Pathway Interaction Database: SMG8
KEGG: SMG8
REACTOME: SMG8
ConsensusPathDB
Pathway Commons: SMG8
MetabolismMetaCyc: SMG8
HUMANCyc: SMG8
RegulationEnsembl's Regulation: ENSG00000167447
miRBase: chr17 :57,287,370-57,292,611
TargetScan: NM_018149
cisRED: ENSG00000167447
ContextiHOP: SMG8
cancer metabolism search in PubMed: SMG8
UCL Cancer Institute: SMG8
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SMG8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMG8
Familial Cancer Database: SMG8
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 613175; gene.
Orphanet
DiseaseKEGG Disease: SMG8
MedGen: SMG8 (Human Medical Genetics with Condition)
ClinVar: SMG8
PhenotypeMGI: SMG8 (International Mouse Phenotyping Consortium)
PhenomicDB: SMG8

Mutations for SMG8
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMG8 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ366984FERMT242116145333120353331277SMG8113183175728861657288686
BU178528SMG84495175729081257290863SMG894951175729042757292476

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=74)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr17:57290673-57290673p.A830V4
chr17:57289008-57289008p.L532L3
chr17:57287454-57287454p.A14A2
chr17:57289010-57289010p.R533Q2
chr17:57288693-57288693p.F427F2
chr17:57290698-57290698p.R838R2
chr17:57288711-57288711p.R433R2
chr17:57288520-57288520p.P370S2
chr17:57292254-57292254p.F956C2
chr17:57288024-57288024p.F204L2

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample163133 5 1  643  1113 11
# mutation163143 5 1  743  1213 13
nonsynonymous SNV163133 5 1  532  510 10
synonymous SNV   1       211  73 3
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr17:57289008p.A830V3
chr17:57290673p.L532L3
chr17:57288520p.F427F2
chr17:57289010p.H439Y2
chr17:57290205p.S674L2
chr17:57288693p.R533Q2
chr17:57288727p.P370S2
chr17:57290351p.N778T1
chr17:57287657p.A959G1
chr17:57288994p.E278Q1

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for SMG8 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for SMG8

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

APPBP2,BPTF,SMG8,CLTC,DHX40,HEATR6,HELZ,
INTS2,MED13,MTMR4,PPM1D,PTRH2,RNF43,RPS6KB1,
SKA2,TLK2,VMP1,TRIM37,TUBD1,USP32,YPEL2
ADNP,SMG8,DIEXF,C2orf44,CRNKL1,DCLRE1A,LSM11,
POLR1B,RBAK,THNSL1,ZBTB5,ZFP3,ZFP62,ZNF17,
ZNF184,ZNF253,ZNF286A,ZNF420,ZNF594,ZNF675,ZNF816

AMZ2,APPBP2,SMG8,C17orf80,CLTC,COIL,DCAF7,
DHX40,GOSR2,INTS2,METTL2A,MGC57346,NOL11,PEX12,
PRR11,RNFT1,RPS6KB1,TLK2,VMP1,TUBD1,USP32
SMG8,CD4,CSF2RA,CSTF1,CYBB,CYSLTR1,CYTH4,
EVI2B,FLI1,GM2A,HLA-DPA1,ITGA4,KBTBD7,PARP11,
PTAFR,TLR1,TLR7,ZNF551,ZNF572,ZNF619,ZXDA
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for SMG8


There's no related Drug.
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Cross referenced IDs for SMG8
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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