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 SUCLG2
Basic gene info.Gene symbolSUCLG2
Gene namesuccinate-CoA ligase, GDP-forming, beta subunit
SynonymsGBETA
CytomapUCSC genome browser: 3p14.1
Genomic locationchr3 :67425140-67705038
Type of geneprotein-coding
RefGenesNM_001177599.1,
NM_003848.3,
Ensembl idENSG00000172340
DescriptionGTP-specific succinyl-CoA synthetase beta subunitGTP-specific succinyl-CoA synthetase subunit betaSCS-betaGsuccinyl-CoA ligase [GDP-forming] subunit beta, mitochondrialsuccinyl-CoA ligase, GDP-forming, beta chain, mitochondrialsuccinyl-CoA synthetase
Modification date20141211
dbXrefs MIM : 603922
HGNC : HGNC
Ensembl : ENSG00000172340
HPRD : 06799
Vega : OTTHUMG00000158740
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_SUCLG2
BioGPS: 8801
Gene Expression Atlas: ENSG00000172340
The Human Protein Atlas: ENSG00000172340
PathwayNCI Pathway Interaction Database: SUCLG2
KEGG: SUCLG2
REACTOME: SUCLG2
ConsensusPathDB
Pathway Commons: SUCLG2
MetabolismMetaCyc: SUCLG2
HUMANCyc: SUCLG2
RegulationEnsembl's Regulation: ENSG00000172340
miRBase: chr3 :67,425,140-67,705,038
TargetScan: NM_001177599
cisRED: ENSG00000172340
ContextiHOP: SUCLG2
cancer metabolism search in PubMed: SUCLG2
UCL Cancer Institute: SUCLG2
Assigned class in ccmGDBC

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Phenotypic Information for SUCLG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: SUCLG2
Familial Cancer Database: SUCLG2
* 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
KEGG_PROPANOATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: SUCLG2
MedGen: SUCLG2 (Human Medical Genetics with Condition)
ClinVar: SUCLG2
PhenotypeMGI: SUCLG2 (International Mouse Phenotyping Consortium)
PhenomicDB: SUCLG2

Mutations for SUCLG2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovarySUCLG2chr36746311567463135SUCLG2chr36746703767467057
ovarySUCLG2chr36748121467481234SUCLG2chr36748241867482438
ovarySUCLG2chr36750907367509093SUCLG2chr36761665467616674
ovarySUCLG2chr36759774267597762chr5129125347129125367
pancreasSUCLG2chr36742779567427815GRID1chr108756940987569429
pancreasSUCLG2chr36743486067434880chr36740133167401351
pancreasSUCLG2chr36749369867493718SUCLG2chr36749680367496823
pancreasSUCLG2chr36760686267606882GRID1chr108757091487570934
pancreasSUCLG2chr36760765867607678chr109352444993524469
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 SUCLG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV660800SUCLG215336745478067454832RBP454403109535376395360750

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 # sample1  1  1 1        
GAIN (# sample)                 
LOSS (# sample)1  1  1 1        
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=11)
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
chr3:67426255-67426255p.I356M2
chr3:67579535-67579535p.K53R2
chr3:67579602-67579602p.E31*2
chr3:67451278-67451278p.?1
chr3:67578595-67578595p.A78A1
chr3:67548572-67548572p.N254T1
chr3:67426240-67426240p.G361G1
chr3:67568750-67568750p.D146G1
chr3:67578634-67578634p.V65V1
chr3:67546277-67546277p.G288D1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   41 3 2  311  45 11
# mutation   41 3 2  311  46 12
nonsynonymous SNV   1  3 2  211  33 10
synonymous SNV   31      1    13 2
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
chr3:67546341p.R381Q,SUCLG22
chr3:67451196p.A315S,SUCLG22
chr3:67546323p.V113V,SUCLG21
chr3:67568743p.D278H,SUCLG21
chr3:67426195p.H105N,SUCLG21
chr3:67579524p.K424N1
chr3:67546326p.N265S,SUCLG21
chr3:67568750p.G103S,SUCLG21
chr3:67426209p.D420N1
chr3:67579530p.G251R,SUCLG21

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 SUCLG2 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 SUCLG2

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

ALDH6A1,APPL1,ARL6IP5,FAM208A,FAM114A2,FYCO1,HNRNPH2,
FAM214A,LRIG1,LZTFL1,NEK4,PDCD6IP,PDE12,PDHB,
RBM47,RYBP,SACM1L,SHQ1,SLMAP,SPCS1,SUCLG2
ADHFE1,ATPAF1,BNIP3,MPC1,TCAIM,CS,DLD,
ETFA,GHITM,GKAP1,GNPAT,HIBADH,IARS2,LACTB2,
NDUFB5,NIPSNAP3B,SDHD,STRADB,SUCLA2,SUCLG2,TMLHE

ABCD3,ACADSB,ARFIP1,BDH1,CPT2,DLD,GFM1,
GPD1L,HADH,AP5M1,OMA1,OXNAD1,PDSS2,PPA2,
RBM47,RPP14,SCP2,SLC30A9,SLC35A3,SUCLG2,UQCRC2
ACAD8,ADH1C,ARL6IP1,COX15,FAM83B,GJB1,IDH1,
KCNE2,MTIF2,AP5M1,NDUFA10,PAFAH2,PAQR5,PCCA,
PDSS2,RNLS,SH2D4A,SLC35F2,STARD7,SUCLG2,XK
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 SUCLG2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00139succinate-CoA ligase, GDP-forming, beta subunitapproved; nutraceuticalSuccinic acid


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Cross referenced IDs for SUCLG2
* 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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