Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	SUCLG2
	Gene name	succinate-CoA ligase, GDP-forming, beta subunit
	Synonyms	GBETA
	Cytomap	UCSC genome browser: 3p14.1
	Genomic location	chr3 :67425140-67705038
	Type of gene	protein-coding
	RefGenes	NM_001177599.1, NM_003848.3,
	Ensembl id	ENSG00000172340
	Description	GTP-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 date	20141211
dbXrefs	MIM : 603922
	HGNC : HGNC
	Ensembl : ENSG00000172340
	HPRD : 06799
	Vega : OTTHUMG00000158740
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SUCLG2
	BioGPS: 8801
	Gene Expression Atlas: ENSG00000172340
	The Human Protein Atlas: ENSG00000172340
Pathway	NCI Pathway Interaction Database: SUCLG2
	KEGG: SUCLG2
	REACTOME: SUCLG2
	ConsensusPathDB
	Pathway Commons: SUCLG2
Metabolism	MetaCyc: SUCLG2
	HUMANCyc: SUCLG2
Regulation	Ensembl's Regulation: ENSG00000172340
	miRBase: chr3 :67,425,140-67,705,038
	TargetScan: NM_001177599
	cisRED: ENSG00000172340
Context	iHOP: SUCLG2
	cancer metabolism search in PubMed: SUCLG2
	UCL Cancer Institute: SUCLG2
Assigned class in ccmGDB	C

Top

Phenotypic Information for SUCLG2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_PROPANOATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE

Others
OMIM
Orphanet
Disease	KEGG Disease: SUCLG2
	MedGen: SUCLG2 (Human Medical Genetics with Condition)
	ClinVar: SUCLG2
Phenotype	MGI: SUCLG2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	SUCLG2	chr3	67463115	67463135	SUCLG2	chr3	67467037	67467057
ovary	SUCLG2	chr3	67481214	67481234	SUCLG2	chr3	67482418	67482438
ovary	SUCLG2	chr3	67509073	67509093	SUCLG2	chr3	67616654	67616674
ovary	SUCLG2	chr3	67597742	67597762		chr5	129125347	129125367
pancreas	SUCLG2	chr3	67427795	67427815	GRID1	chr10	87569409	87569429
pancreas	SUCLG2	chr3	67434860	67434880		chr3	67401331	67401351
pancreas	SUCLG2	chr3	67493698	67493718	SUCLG2	chr3	67496803	67496823
pancreas	SUCLG2	chr3	67606862	67606882	GRID1	chr10	87570914	87570934
pancreas	SUCLG2	chr3	67607658	67607678		chr10	93524449	93524469

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SUCLG2 related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

AV660800

SUCLG2

67454780

67454832

RBP4

403

95353763

95360750

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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)

Top

SNV 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

Top

Somatic 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.

Top

Top 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 position	Mutation(aa)	Unique sampleID count
chr3:67426255-67426255	p.I356M	2
chr3:67579535-67579535	p.K53R	2
chr3:67579602-67579602	p.E31*	2
chr3:67548558-67548558	p.V259M	1
chr3:67568743-67568743	p.F148F	1
chr3:67451278-67451278	p.?	1
chr3:67578595-67578595	p.A78A	1
chr3:67548572-67548572	p.N254T	1
chr3:67426240-67426240	p.G361G	1
chr3:67568750-67568750	p.D146G	1

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				4	1		3		2			3	1	1			4	5		11
# mutation				4	1		3		2			3	1	1			4	6		12
nonsynonymous SNV				1			3		2			2	1	1			3	3		10
synonymous SNV				3	1							1					1	3		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])

Top

Top 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 Position	Mutation(aa)	Unique sampleID count
chr3:67546341	p.R381Q,SUCLG2	2
chr3:67451196	p.A315S,SUCLG2	2
chr3:67568692	p.A313V,SUCLG2	1
chr3:67578634	p.Q129R,SUCLG2	1
chr3:67546323	p.N302T,SUCLG2	1
chr3:67568743	p.A126A,SUCLG2	1
chr3:67426195	p.D278H,SUCLG2	1
chr3:67579524	p.V113V,SUCLG2	1
chr3:67546326	p.K424N	1
chr3:67568750	p.N265S,SUCLG2	1

Other 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

Copy 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]

Top

Gene Expression for SUCLG2

Gene 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.

Differential 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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

Gene-Gene Network Information

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

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

Top

Pharmacological Information for SUCLG2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00139	succinate-CoA ligase, GDP-forming, beta subunit	approved; nutraceutical	Succinic acid

Top

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