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

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 SUCLG1

Basic gene info.	Gene symbol	SUCLG1
	Gene name	succinate-CoA ligase, alpha subunit
	Synonyms	GALPHA\|MTDPS9\|SUCLA1
	Cytomap	UCSC genome browser: 2p11.2
	Genomic location	chr2 :84650646-84686586
	Type of gene	protein-coding
	RefGenes	NM_003849.3,
	Ensembl id	ENSG00000163541
	Description	SCS-alphasuccinyl-CoA ligase [ADP/GDP-forming] subunit alpha, mitochondrialsuccinyl-CoA ligase [GDP-forming] subunit alpha, mitochondrialsuccinyl-CoA synthetase subunit alpha
	Modification date	20141207
dbXrefs	MIM : 611224
	HGNC : HGNC
	Ensembl : ENSG00000163541
	HPRD : 18128
	Vega : OTTHUMG00000130023
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_SUCLG1
	BioGPS: 8802
	Gene Expression Atlas: ENSG00000163541
	The Human Protein Atlas: ENSG00000163541
Pathway	NCI Pathway Interaction Database: SUCLG1
	KEGG: SUCLG1
	REACTOME: SUCLG1
	ConsensusPathDB
	Pathway Commons: SUCLG1
Metabolism	MetaCyc: SUCLG1
	HUMANCyc: SUCLG1
Regulation	Ensembl's Regulation: ENSG00000163541
	miRBase: chr2 :84,650,646-84,686,586
	TargetScan: NM_003849
	cisRED: ENSG00000163541
Context	iHOP: SUCLG1
	cancer metabolism search in PubMed: SUCLG1
	UCL Cancer Institute: SUCLG1
Assigned class in ccmGDB	C

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Phenotypic Information for SUCLG1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: SUCLG1
	Familial Cancer Database: SUCLG1

* 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: SUCLG1
	MedGen: SUCLG1 (Human Medical Genetics with Condition)
	ClinVar: SUCLG1
Phenotype	MGI: SUCLG1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: SUCLG1

Mutations for SUCLG1

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SUCLG1 related fusion information.

ID	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
BP319935	SP100	2	265	2	231280936	231307732	SUCLG1	258	339	2	84650652	84650733
BM968054	SUCLG1	5	170	2	84650857	84652664	SUCLG1	167	420	2	84658640	84668196
BU607293	SUCLG1	5	170	2	84650857	84652664	SUCLG1	167	420	2	84658640	84668196

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=11)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=2)

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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
chr2:84658736-84658736	p.E241K	4
chr2:84652606-84652606	p.S316F	3
chr2:84652539-84652539	p.K338K	2
chr2:84676841-84676841	p.A45T	2
chr2:84668577-84668577	p.E109*	1
chr2:84658638-84658638	p.H273H	1
chr2:84686333-84686337	p.G20fs*32	1
chr2:84660507-84660507	p.T214T	1
chr2:84670410-84670410	p.E106*	1
chr2:84652548-84652548	p.T335T	1

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SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

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	1			3	2				6			4		1			2	5		3
# mutation	1			3	2				6			4		1			2	5		3
nonsynonymous SNV	1			1	2				4			2					2	2		2
synonymous SNV				2					2			2		1				3		1

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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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
chr2:84652566	p.V140G	1
chr2:84660507	p.A132D	1
chr2:84670519	p.P329P	1
chr2:84652567	p.A127A	1
chr2:84668224	p.P329H	1
chr2:84676834	p.A125A	1
chr2:84652596	p.Q319H	1
chr2:84668385	p.L98S	1
chr2:84676841	p.G301W	1
chr2:84652652	p.G91E	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 SUCLG1 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 SUCLG1

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))

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CNV 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

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


ATP5G3,ATP5O,BOLA3,PRADC1,CCT4,CCT7,COMMD1, COX5A,COX7B,DGUOK,IMMT,KCMF1,MDH1,MDH2, MRPS5,NDUFB3,RNF181,SF3B14,SNRPG,SUCLG1,VAMP8	APIP,BNIP3,CS,DECR1,DLST,GBE1,GPI, HADH,MLX,MARC2,MRPS15,NDUFB5,NFU1,PDHA1, PFKFB1,PPP1R1A,PRDX6,RNF157,STBD1,SUCLG1,EMC3

ATP5C1,ATP5F1,ATP5G3,ATP5L,C2orf47,PRADC1,COX5A, COX5B,COX7A2,COX7A2L,DBI,FAM96A,MDH1,MEMO1, MRPL11,MRPL22,MRPL35,NDUFS3,PDSS1,SDHD,SUCLG1	AK2,ATP5C1,ATPIF1,MPC2,C2orf47,CENPV,CRYL1, FAM96A,GLOD4,IMP3,MGST2,MRPL48,MTCH2,NDUFC2, OXNAD1,RARS2,SAR1B,SDHAF2,SDHB,SUCLG1,TMEM106C

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

: Open all plots for all cancer types

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Interacting 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 SUCLG1

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, alpha subunit	approved; nutraceutical	Succinic acid

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Cross referenced IDs for SUCLG1

* 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