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 SMG7
Basic gene info.Gene symbolSMG7
Gene nameSMG7 nonsense mediated mRNA decay factor
SynonymsC1orf16|EST1C|SGA56M
CytomapUCSC genome browser: 1q25
Genomic locationchr1 :183441505-183523328
Type of geneprotein-coding
RefGenesNM_001174061.1,
NM_173156.2,NM_201568.2,NM_201569.2,NM_014837.3,
Ensembl idENSG00000116698
DescriptionEST1 telomerase component homolog CEST1-like protein Cbreast cancer-associated antigen SGA-56Mever shorter telomeres 1Cprotein SMG7smg-7 homolog, nonsense mediated mRNA decay factor
Modification date20141207
dbXrefs MIM : 610964
HGNC : HGNC
Ensembl : ENSG00000116698
HPRD : 10723
Vega : OTTHUMG00000035221
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SMG7
BioGPS: 9887
Gene Expression Atlas: ENSG00000116698
The Human Protein Atlas: ENSG00000116698
PathwayNCI Pathway Interaction Database: SMG7
KEGG: SMG7
REACTOME: SMG7
ConsensusPathDB
Pathway Commons: SMG7
MetabolismMetaCyc: SMG7
HUMANCyc: SMG7
RegulationEnsembl's Regulation: ENSG00000116698
miRBase: chr1 :183,441,505-183,523,328
TargetScan: NM_001174061
cisRED: ENSG00000116698
ContextiHOP: SMG7
cancer metabolism search in PubMed: SMG7
UCL Cancer Institute: SMG7
Assigned class in ccmGDBC

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Phenotypic Information for SMG7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SMG7
Familial Cancer Database: SMG7
* 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
Orphanet
DiseaseKEGG Disease: SMG7
MedGen: SMG7 (Human Medical Genetics with Condition)
ClinVar: SMG7
PhenotypeMGI: SMG7 (International Mouse Phenotyping Consortium)
PhenomicDB: SMG7

Mutations for SMG7
* 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
pancreasSMG7chr1183448375183448395chr1183425116183425136
pancreasSMG7chr1183448377183448397chr1183425116183425136
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 SMG7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF872191SMG711711183457369183457540HNRNPF164302104388593443886072
AA598525SMG713381183522990183523326SMG73354781183522874183523017
H80346SMG71291183463921183463949FBXL2013288173752593437526469
BI014023CDK131131374004275240043102SMG72995081183512092183512301

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   1      3      
GAIN (# sample)   1      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=25)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=0)
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
chr1:183495729-183495729p.?7
chr1:183502837-183502837p.C345R4
chr1:183520210-183520210p.S1062L3
chr1:183514093-183514093p.P672P2
chr1:183510196-183510196p.R458H2
chr1:183514444-183514444p.Q789Q2
chr1:183511583-183511583p.K596N2
chr1:183495733-183495733p.L105F2
chr1:183510237-183510237p.R472G2
chr1:183498545-183498545p.V240V2

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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
# sample32 143 2 2  9102 1112114
# mutation42 123 2 2  10102 1112116
nonsynonymous SNV41 91 1 2  991 192112
synonymous SNV 1 32 1    111  2  4
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
chr1:183502837p.C303R,SMG74
chr1:183520210p.H673Y,SMG71
chr1:183498122p.P865H,SMG71
chr1:183514071p.R267C,SMG71
chr1:183515189p.R489Q,SMG71
chr1:183506328p.M687I,SMG71
chr1:183518360p.K928N,SMG71
chr1:183511445p.Q283H,SMG71
chr1:183520213p.N508N,SMG71
chr1:183498158p.P697R,SMG71

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 SMG7 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 SMG7

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

AHCTF1,PRRC2C,SPRTN,BROX,SUCO,CAMSAP2,CDC73,
CEP350,DHX9,FAM20B,FLVCR1,IPO9,RAB3GAP2,RBBP5,
SLC25A44,SMG7,STX6,TADA1,TOR1AIP2,TPR,TROVE2
ARID2,PRR14L,CNOT1,AGO1,HEATR1,MGA,NF1,
RNF111,SMG7,STX17,TNKS,TUG1,ZMYM4,ZKSCAN8,
ZNF253,ZNF420,ZNF510,ZNF585A,ZNF616,ZNF623,ZNF81

ARHGEF11,ASH1L,PRRC2C,BCL9,CEP350,GON4L,HEATR1,
LPGAT1,MTR,NCOA6,POGK,RAB3GAP2,RPRD2,SETDB1,
SMG7,STX6,TP53BP2,UBAP2L,UBE2Q1,ZC3H11A,ZNF687
AKAP13,BIRC6,CDK13,FOXJ3,FOXO3B,GBF1,GOLGB1,
IGF2R,KDM2A,NCOR1,NF1,NIPBL,RALGAPB,SMG7,
SON,SPEN,TNRC6B,UBN1,UBR4,UPF1,USP9X
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 SMG7


There's no related Drug.
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Cross referenced IDs for SMG7
* 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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