Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 SMG5
Basic gene info.Gene symbolSMG5
Gene nameSMG5 nonsense mediated mRNA decay factor
SynonymsEST1B|LPTS-RP1|LPTSRP1|SMG-5
CytomapUCSC genome browser: 1q21.2
Genomic locationchr1 :156219014-156252620
Type of geneprotein-coding
RefGenesNM_015327.2,
Ensembl idENSG00000198952
DescriptionEST1 telomerase component homolog BEST1-like protein BEst1p-like protein BLPTS interacting proteinLPTS-interacting proteinRP11-54H19.7ever shorter telomeres 1BhSMG-5protein SMG5smg-5 homolog, nonsense mediated mRNA decay factor
Modification date20141207
dbXrefs MIM : 610962
HGNC : HGNC
Ensembl : ENSG00000198952
HPRD : 16869
Vega : OTTHUMG00000017491
ProteinUniProt: Q9UPR3
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMG5
BioGPS: 23381
Gene Expression Atlas: ENSG00000198952
The Human Protein Atlas: ENSG00000198952
PathwayNCI Pathway Interaction Database: SMG5
KEGG: SMG5
REACTOME: SMG5
ConsensusPathDB
Pathway Commons: SMG5
MetabolismMetaCyc: SMG5
HUMANCyc: SMG5
RegulationEnsembl's Regulation: ENSG00000198952
miRBase: chr1 :156,219,014-156,252,620
TargetScan: NM_015327
cisRED: ENSG00000198952
ContextiHOP: SMG5
cancer metabolism search in PubMed: SMG5
UCL Cancer Institute: SMG5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for SMG5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMG5
Familial Cancer Database: SMG5
* 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 610962; gene.
Orphanet
DiseaseKEGG Disease: SMG5
MedGen: SMG5 (Human Medical Genetics with Condition)
ClinVar: SMG5
PhenotypeMGI: SMG5 (International Mouse Phenotyping Consortium)
PhenomicDB: SMG5

Mutations for SMG5
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovarySMG5chr1156245435156245455SMG5chr1156232768156232788
pancreasSMG5chr1156228890156228910SMG5chr1156228998156229018
pancreasSMG5chr1156239733156239753SMG5chr1156224548156224568
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SMG5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA313406SMG51771156246875156246950OFD175302X1376936613770928
BQ335493SMG5223251156242151156246960DIDO1321382206154114861541209

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample          3      
GAIN (# sample)          3      
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=71)
Stat. for Synonymous SNVs
(# total SNVs=24)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr1:156238160-156238160p.R254W3
chr1:156238081-156238081p.R280Q2
chr1:156235769-156235769p.N553S2
chr1:156230371-156230371p.E718E2
chr1:156247778-156247778p.E79K2
chr1:156236063-156236063p.R455H2
chr1:156235781-156235781p.P549L2
chr1:156244415-156244415p.R173*2
chr1:156230268-156230268p.R753W2
chr1:156233189-156233189p.A676A2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample64 141 5 21 1232 11014 13
# mutation84 151 6 21 1532 11014 15
nonsynonymous SNV54 101 3 11 82   511 9
synonymous SNV3  5  3 1  712 153 6
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
chr1:156244428p.E718E2
chr1:156238159p.Q168Q2
chr1:156244470p.K154N2
chr1:156238160p.F793F2
chr1:156228859p.R455H2
chr1:156236063p.R770C2
chr1:156230371p.R254Q2
chr1:156228930p.R753W2
chr1:156235910p.R254W2
chr1:156230268p.T506M2

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 SMG5 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 SMG5

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

ARHGEF11,CCT3,CDCA2,CKS1B,DENND4B,DPH2,FAM189B,
FLAD1,GPATCH4,GTPBP4,HDGF,ILF2,IQGAP3,IRAK1,
ISG20L2,PI4KB,PLK1,PRCC,SMG5,UBQLN4,VPS72
ABCF3,BAP1,BAG6,RABL6,DGKZ,DHX16,EVI5L,
INPPL1,INTS1,POLRMT,PTCD1,RAB11FIP3,RPTOR,PPP6R2,
SBF1,SH3BP5L,SMG5,SPG7,STK11,USP5,ZNF76

ARHGEF11,ASXL1,CEP250,DENND4B,DIDO1,DNAJC5,GMEB2,
GON4L,INTS1,JRK,LSM14B,MAFG,MLLT6,SLC9A8,
SMG5,SS18L1,TAF4,ZGPAT,ZHX3,ZNF335,ZNF687
AP3D1,CLEC16A,DEPDC5,DHX16,DPP9,EDC4,FBXL18,
GBF1,GOLGA3,KDM2A,CEP170B,MYO18A,PCNXL3,SMG5,
SMG7,SMURF1,SP2,TAOK2,UBN1,UPF1,XPO6
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 SMG5


There's no related Drug.
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Cross referenced IDs for SMG5
* 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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