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 CS

Basic gene info.	Gene symbol	CS
	Gene name	citrate synthase
	Synonyms	-
	Cytomap	UCSC genome browser: 12q13.2
	Genomic location	chr12 :56665482-56694175
	Type of gene	protein-coding
	RefGenes	NM_004077.2, NM_198324.1,
	Ensembl id	ENSG00000062485
	Description	citrate (Si)-synthasecitrate synthase, mitochondrial
	Modification date	20141207
dbXrefs	MIM : 118950
	HGNC : HGNC
	Ensembl : ENSG00000062485
	HPRD : 00349
	Vega : OTTHUMG00000170344
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CS
	BioGPS: 1431
	Gene Expression Atlas: ENSG00000062485
	The Human Protein Atlas: ENSG00000062485
Pathway	NCI Pathway Interaction Database: CS
	KEGG: CS
	REACTOME: CS
	ConsensusPathDB
	Pathway Commons: CS
Metabolism	MetaCyc: CS
	HUMANCyc: CS
Regulation	Ensembl's Regulation: ENSG00000062485
	miRBase: chr12 :56,665,482-56,694,175
	TargetScan: NM_004077
	cisRED: ENSG00000062485
Context	iHOP: CS
	cancer metabolism search in PubMed: CS
	UCL Cancer Institute: CS
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: CS
	Familial Cancer Database: CS

* 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_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_METABOLISM_OF_PROTEINS

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

Mutations for CS

* 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

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	CS	chr12	56677873	56677893	WIBG	chr12	56317814	56317834
pancreas	CS	chr12	56683700	56683720	CS	chr12	56685200	56685220

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 CS 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
DB135857	CAPN1	1	168	11	64949214	64949381	CS	169	540	12	56677599	56694113
BM766816	MRPL30	1	358	2	99813719	99814077	CS	359	447	12	56667481	56667569
AI336282	CS	11	335	12	56665485	56665809	SUPT16H	329	514	14	21828574	21829071

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=37)	Stat. for Synonymous SNVs (# total SNVs=8)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted snv.

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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
chr12:56676244-56676244	p.R183Q	4
chr12:56669910-56669910	p.L220I	4
chr12:56676232-56676232	p.Q187R	3
chr12:56676208-56676208	p.W195*	2
chr12:56676769-56676769	p.R92S	2
chr12:56668908-56668908	p.E266K	2
chr12:56676220-56676220	p.R191Q	1
chr12:56667537-56667537	p.P355L	1
chr12:56677608-56677608	p.V79I	1
chr12:56668910-56668910	p.H265L	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=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	2	1		2			2		3			1	1	1			2	4		7
# mutation	2	1		2			2		3			1	1	1			2	4		8
nonsynonymous SNV	1	1					2		2			1		1			1	2		7
synonymous SNV	1			2					1				1				1	2		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
chr12:56668847	p.A229T	1
chr12:56676252	p.S225S	1
chr12:56668876	p.E223K	1
chr12:56676726	p.K215N	1
chr12:56669791	p.N400S	1
chr12:56677608	p.I206I	1
chr12:56667402	p.L365L	1
chr12:56669802	p.Q187R	1
chr12:56677625	p.T358T	1
chr12:56667506	p.A186T	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 CS 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 CS

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


ARL10,CHST3,CMTM5,COL4A2,CSPG4,EVX2,EXTL1, EVA1A,FAM19A3,GPX6,HAPLN4,LIX1,MFGE8,NRXN2, PMP2,RLBP1,SHC4,SOX6,TIAM2,TRPV4,UBL4B	ABHD15,ACACB,AFAP1L1,AGPAT2,ALDH1L1,AQP7P1,C14orf180, CAMK1,CEBPA,CIDEC,COL4A2,CSPG4,ITGA7,LIPE, MLXIPL,PC,PKDCC,PLA2G16,PNPLA2,RXRA,TMEM132C

ARHGEF17,CNTNAP1,CSPG4,CXorf36,DAAM2,DIXDC1,EHD2, FAM129A,FILIP1,GJC1,HSPG2,ITGB3,JPH2,KIAA1462, MAP1A,MAP1B,MCAM,MMRN2,MRVI1,MSRB3,TGFB1I1	ADARB1,AHNAK2,COL4A1,CSPG4,DCHS1,DMD,DOCK3, EHD2,EVC,FRMPD4,FYCO1,GLI2,LAMA5,LAMB2, MAP4,NBEA,POU3F4,PRICKLE2,RNF150,RYR3,TEAD1

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 CS

There's no related Drug.

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Cross referenced IDs for CS

* 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