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 COASY

Basic gene info.	Gene symbol	COASY
	Gene name	CoA synthase
	Synonyms	DPCK\|NBIA6\|NBP\|PPAT\|UKR1\|pOV-2
	Cytomap	UCSC genome browser: 17q12-q21
	Genomic location	chr17 :40714091-40718295
	Type of gene	protein-coding
	RefGenes	NM_001042529.2, NM_001042532.3,NM_025233.6,NM_001042530.1,NM_001042531.1,
	Ensembl id	ENSG00000068120
	Description	bifunctional coenzyme A synthasebifunctional phosphopantetheine adenylyl transferase/dephospho CoA kinasenucleotide binding proteinphosphopantetheine adenylyltransferase / dephosphocoenzyme A kinase
	Modification date	20141207
dbXrefs	MIM : 609855
	HGNC : HGNC
	Ensembl : ENSG00000068120
	HPRD : 13080
	Vega : OTTHUMG00000180245
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_COASY
	BioGPS: 80347
	Gene Expression Atlas: ENSG00000068120
	The Human Protein Atlas: ENSG00000068120
Pathway	NCI Pathway Interaction Database: COASY
	KEGG: COASY
	REACTOME: COASY
	ConsensusPathDB
	Pathway Commons: COASY
Metabolism	MetaCyc: COASY
	HUMANCyc: COASY
Regulation	Ensembl's Regulation: ENSG00000068120
	miRBase: chr17 :40,714,091-40,718,295
	TargetScan: NM_001042529
	cisRED: ENSG00000068120
Context	iHOP: COASY
	cancer metabolism search in PubMed: COASY
	UCL Cancer Institute: COASY
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: COASY
	Familial Cancer Database: COASY

* 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
REACTOME_METABOLISM_OF_VITAMINS_AND_COFACTORS

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

Mutations for COASY

* 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 COASY 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
AI650663	COASY	12	126	17	40718187	40718301	PPAN	120	378	19	10220859	10221276
BP275946	COASY	1	437	17	40714169	40714997	LOC100507412	430	499	?	109705	109774
DC383781	TAF1D	1	64	11	93465527	93465590	COASY	65	563	17	40714169	40714791
BG120370	COASY	1	61	17	40716721	40716794	COASY	52	757	17	40716816	40718145
BE252620	COASY	1	266	17	40716570	40717050	DTD1	264	586	20	18576749	18725309
BQ212022	COASY	14	115	17	40716721	40716835	COASY	106	849	17	40716816	40718161
CR739363	COASY	1	194	17	40714187	40714380	PPAN	189	483	19	10218787	10220884

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

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

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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=35)	Stat. for Synonymous SNVs (# total SNVs=11)

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

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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
chr17:40714723-40714723	p.S28L	3
chr17:40714959-40714959	p.L107F	2
chr17:40716901-40716901	p.E408Q	2
chr17:40714961-40714961	p.L107L	2
chr17:40716022-40716022	p.V248V	2
chr17:40714916-40714916	p.T92T	1
chr17:40716813-40716813	p.L378L	1
chr17:40715174-40715174	p.S178S	1
chr17:40717505-40717505	p.V468V	1
chr17:40714664-40714665	p.(=)	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	2	3	2	5			2		3	1		7	3	2		1	3	2		10
# mutation	2	3	2	4			2		3	1		7	3	2		1	3	2		11
nonsynonymous SNV	1	2	1	3			1		2			6	1	2			2	1		10
synonymous SNV	1	1	1	1			1		1	1		1	2			1	1	1		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
chr17:40717718	p.R429W,COASY	2
chr17:40717048	p.Y359C,COASY	2
chr17:40716755	p.A509A,COASY	2
chr17:40714959	p.L8L,COASY	1
chr17:40717709	p.S178S,COASY	1
chr17:40716081	p.L378L,COASY	1
chr17:40714664	p.R21G,COASY	1
chr17:40716813	p.G197D,COASY	1
chr17:40714971	p.A383A,COASY	1
chr17:40716143	p.A23V,COASY	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 COASY 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 COASY

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


AARSD1,ACBD4,BECN1,CCDC103,COA3,CHCHD5,COASY, FAM134C,G6PC3,GAMT,GHDC,HEXIM2,KAT2A,KRT19, NAGLU,PLEKHH3,RAB5C,SLC25A39,STK16,TMUB2,VPS25	ARRDC1,ATP13A1,ATP13A2,HID1,C9orf114,CACFD1,COASY, COMT,COQ4,DAK,DUS1L,FUK,GAK,GSS, IGSF8,LLGL2,NARFL,NDOR1,PAK4,PICK1,SGSM3

AARSD1,CCDC137,CDC6,COASY,DBF4B,DUS1L,EFTUD2, ERAL1,GIT1,GPS1,KAT2A,MLX,MRM1,PNPO, POLDIP2,SLC25A19,SLC25A39,SMARCD2,TSEN54,TUBG1,VPS25	ABCF3,AP1M2,APEH,APEX2,ARHGEF16,CKMT1B,COASY, E2F2,FBXL6,SLC52A2,IRAK1,LEMD2,PITPNM1,SH3BP1, SLC25A10,SMARCD2,STXBP2,TALDO1,TLCD1,TTLL12,USP43

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 COASY

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
DB00151	CoA synthase	approved; nutraceutical	L-Cysteine

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Cross referenced IDs for COASY

* 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