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 CDS2

Basic gene info.	Gene symbol	CDS2
	Gene name	CDP-diacylglycerol synthase (phosphatidate cytidylyltransferase) 2
	Synonyms	-
	Cytomap	UCSC genome browser: 20p13
	Genomic location	chr20 :5107406-5178533
	Type of gene	protein-coding
	RefGenes	NM_003818.3,
	Ensembl id	ENSG00000101290
	Description	CDP-DAG synthase 2CDP-DG synthase 2CDP-DG synthetase 2CDP-diacylglycerol synthase 2CDP-diglyceride diphosphorylase 2CDP-diglyceride pyrophosphorylase 2CDP-diglyceride synthase 2CDP-diglyceride synthetase 2CDS 2CTP:phosphatidate cytidylyltransfera
	Modification date	20141207
dbXrefs	MIM : 603549
	HGNC : HGNC
	Ensembl : ENSG00000101290
	HPRD : 09150
	Vega : OTTHUMG00000031801
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CDS2
	BioGPS: 8760
	Gene Expression Atlas: ENSG00000101290
	The Human Protein Atlas: ENSG00000101290
Pathway	NCI Pathway Interaction Database: CDS2
	KEGG: CDS2
	REACTOME: CDS2
	ConsensusPathDB
	Pathway Commons: CDS2
Metabolism	MetaCyc: CDS2
	HUMANCyc: CDS2
Regulation	Ensembl's Regulation: ENSG00000101290
	miRBase: chr20 :5,107,406-5,178,533
	TargetScan: NM_003818
	cisRED: ENSG00000101290
Context	iHOP: CDS2
	cancer metabolism search in PubMed: CDS2
	UCL Cancer Institute: CDS2
Assigned class in ccmGDB	C

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Phenotypic Information for CDS2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CDS2
	Familial Cancer Database: CDS2

* 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_GLYCEROPHOSPHOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: CDS2
	MedGen: CDS2 (Human Medical Genetics with Condition)
	ClinVar: CDS2
Phenotype	MGI: CDS2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CDS2

Mutations for CDS2

* 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

* 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	CDS2	chr20	5135500	5135520		chr8	30642406	30642426
ovary	CDS2	chr20	5165218	5165238	CDS2	chr20	5165357	5165377
ovary	CDS2	chr20	5169003	5169023		chr20	3023744	3023764

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 CDS2 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
DN999202	CDS2	9	493	20	5175804	5176289	CRK	487	584	17	1325691	1325788
CB052191	UBXN11	29	212	1	26608773	26608980	CDS2	207	530	20	5172014	5172338
BI020398	PIK3CD	118	141	1	9784241	9784264	CDS2	125	423	20	5173732	5174032

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=22)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted 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
chr20:5169729-5169729	p.Y333F	2
chr20:5170424-5170424	p.R382H	2
chr20:5170471-5170471	p.A398T	2
chr20:5159548-5159548	p.L159V	1
chr20:5166428-5166428	p.G262C	1
chr20:5155926-5155926	p.?	1
chr20:5170746-5170746	p.?	1
chr20:5159590-5159590	p.L173V	1
chr20:5167438-5167438	p.L312L	1
chr20:5157302-5157302	p.C100C	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	1	9			2		1			5	1				6	2	1	1
# mutation	1	3	1	8			2		1			6	1				6	2	1	1
nonsynonymous SNV		2	1	7			2		1			4					4	2	1	1
synonymous SNV	1	1		1								2	1				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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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
chr20:5170424	p.R382H	2
chr20:5165556	p.L159V	1
chr20:5157335	p.A341V	1
chr20:5165585	p.R160Q	1
chr20:5170443	p.K361N	1
chr20:5157336	p.T172I	1
chr20:5165588	p.L173V	1
chr20:5170471	p.L388L	1
chr20:5157348	p.L175V	1
chr20:5166422	p.A398T	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 CDS2 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 CDS2

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


ACADSB,ATRN,TMEM230,CDS2,CHD6,CRNKL1,CSNK2A1, DMXL1,FASTKD5,LOC647979,MAVS,KAT6B,NRSN2,PANK2, PSMF1,PTPRA,SDC4,SRXN1,SYS1,TBC1D20,ZNF44	ABHD12B,BCL2,BMPR2,C6orf120,TMEM245,CDS2,CHRNA9, FAM172A,GFPT1,GNG12,EFCAB14,LOC647979,MKL2,NHS, OCRL,PIK3CB,RNF180,SEL1L,SERINC3,VPS41,WFDC11

ANKEF1,C20orf196,AP5S1,TMEM230,CDS2,CRLS1,CSNK2A1, CSNK2A3,DSTN,NSFL1C,PANK2,PSMF1,PTPRA,SNRPB2, STK35,TASP1,TBC1D20,TRMT6,UBOX5,VPS16,ZCCHC3	ADAM11,SKIDA1,CCKBR,CDS2,CNTNAP5,DCAF12L2,FABP3, SUPT20HL2,GDF5,HOXB2,KCNE1,KLHL10,LMO3,LOC100192378, LOC400804,NOS1,ODAM,RARB,SLC2A4,THAP8,TMEM200B

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 CDS2

There's no related Drug.

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Cross referenced IDs for CDS2

* 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