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 CDA

Basic gene info.	Gene symbol	CDA
	Gene name	cytidine deaminase
	Synonyms	CDD
	Cytomap	UCSC genome browser: 1p36.2-p35
	Genomic location	chr1 :20915443-20945400
	Type of gene	protein-coding
	RefGenes	NM_001785.2,
	Ensembl id	ENSG00000158825
	Description	cytidine aminohydrolasecytosine nucleoside deaminasesmall cytidine deaminase
	Modification date	20141222
dbXrefs	MIM : 123920
	HGNC : HGNC
	Ensembl : ENSG00000158825
	HPRD : 11744
	Vega : OTTHUMG00000002845
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CDA
	BioGPS: 978
	Gene Expression Atlas: ENSG00000158825
	The Human Protein Atlas: ENSG00000158825
Pathway	NCI Pathway Interaction Database: CDA
	KEGG: CDA
	REACTOME: CDA
	ConsensusPathDB
	Pathway Commons: CDA
Metabolism	MetaCyc: CDA
	HUMANCyc: CDA
Regulation	Ensembl's Regulation: ENSG00000158825
	miRBase: chr1 :20,915,443-20,945,400
	TargetScan: NM_001785
	cisRED: ENSG00000158825
Context	iHOP: CDA
	cancer metabolism search in PubMed: CDA
	UCL Cancer Institute: CDA
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: CDA
	Familial Cancer Database: CDA

* 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_PYRIMIDINE_METABOLISM KEGG_DRUG_METABOLISM_OTHER_ENZYMES REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PYRIMIDINE_METABOLISM

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

Mutations for CDA

* 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 CDA 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
BM850111	NEDD8-MDP1	1	512	14	24686165	24701571	CDA	507	570	1	20945065	20945128
BU634160	CDA	40	218	1	20923871	21310549	GNPTAB	213	718	12	102140628	102147173
BF901504	CCHCR1	1	367	6	2409347	2413749	CDA	368	461	1	20938233	20938325

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=19)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr1:20915701-20915701	p.K27Q	2
chr1:20931527-20931527	p.I87I	2
chr1:20931489-20931489	p.V75I	2
chr1:20931490-20931490	p.V75A	2
chr1:20945033-20945033	p.G138E	2
chr1:20945046-20945046	p.L142L	1
chr1:20931520-20931520	p.I85T	1
chr1:20945055-20945055	p.T145T	1
chr1:20915759-20915760	p.R48fs*20	1
chr1:20915772-20915772	p.F50F	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=3

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

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
chr1:20931490	p.V75A	2
chr1:20931499	p.G138E	1
chr1:20931506	p.L10L	1
chr1:20931520	p.L18L	1
chr1:20931527	p.F50F	1
chr1:20931528	p.P61Q	1
chr1:20915652	p.V75I	1
chr1:20944968	p.G78E	1
chr1:20915674	p.K80N	1
chr1:20944973	p.I85T	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 CDA 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 CDA

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


CALB1,CCL24,CDA,COL7A1,CSF2,DEFB103B,IFNK, IL1A,KRT14,KRT6A,KRT6C,KRTAP11-1,LAMC2,SFN, SPINK7,SPRR1B,TMPRSS11D,TRIML2,UCN2,WNT7A,ZBED2	C1QTNF2,C1QTNF3,CD70,CDA,CLEC10A,DNM1,EMP3, FBN1,FOLR2,FSTL1,GFPT2,GPR133,HRH1,HTRA3, LGI2,LMX1A,MFAP5,PROCR,SPSB4,WNT10B,XPNPEP2

LINC00520,C16orf74,CDA,DHRS9,ELOVL1,EMP1,FAM25A, FAM25BP,GJB3,GJB4,KLK8,KRT19,LAMA3,LAMB3, LOC100216001,PLIN3,POLD4,PXN,RHOD,RHOF,SLC2A1	C11orf86,C1orf177,CDA,CLCA4,CLTB,DIRC2,GUCA2A, HIST1H1C,KRT8,PLA2G2F,PLIN3,POLD4,RHBDF1,RHOC, RHOG,SAMD9,SH3BGRL3,SIRT6,TSPAN1,UNC13D,ZNF622

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 CDA

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
DB00987	cytidine deaminase	approved; investigational	Cytarabine
DB01101	cytidine deaminase	approved; investigational	Capecitabine
DB00544	cytidine deaminase	approved	Fluorouracil
DB02745	cytidine deaminase	experimental	Uridine
DB00928	cytidine deaminase	approved; investigational	Azacitidine
DB00313	cytidine deaminase	approved; investigational	Valproic Acid
DB00441	cytidine deaminase	approved	Gemcitabine
DB00515	cytidine deaminase	approved	Cisplatin

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Cross referenced IDs for CDA

* 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