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 CES2

Basic gene info.	Gene symbol	CES2
	Gene name	carboxylesterase 2
	Synonyms	CE-2\|CES2A1\|PCE-2\|iCE
	Cytomap	UCSC genome browser: 16q22.1
	Genomic location	chr16 :66968346-66978994
	Type of gene	protein-coding
	RefGenes	NM_003869.5, NM_198061.2,NR_036684.1,
	Ensembl id	ENSG00000172831
	Description	carboxylesterase 2 (intestine, liver)cocaine esterasehCE-2intestinal carboxylesterase; liver carboxylesterase-2methylumbelliferyl-acetate deacetylase 2
	Modification date	20141207
dbXrefs	MIM : 605278
	HGNC : HGNC
	Ensembl : ENSG00000172831
	HPRD : 07062
	Vega : OTTHUMG00000137517
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CES2
	BioGPS: 8824
	Gene Expression Atlas: ENSG00000172831
	The Human Protein Atlas: ENSG00000172831
Pathway	NCI Pathway Interaction Database: CES2
	KEGG: CES2
	REACTOME: CES2
	ConsensusPathDB
	Pathway Commons: CES2
Metabolism	MetaCyc: CES2
	HUMANCyc: CES2
Regulation	Ensembl's Regulation: ENSG00000172831
	miRBase: chr16 :66,968,346-66,978,994
	TargetScan: NM_003869
	cisRED: ENSG00000172831
Context	iHOP: CES2
	cancer metabolism search in PubMed: CES2
	UCL Cancer Institute: CES2
Assigned class in ccmGDB	C

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Phenotypic Information for CES2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: CES2
	Familial Cancer Database: CES2

* 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_DRUG_METABOLISM_OTHER_ENZYMES

Others
OMIM
Orphanet
Disease	KEGG Disease: CES2
	MedGen: CES2 (Human Medical Genetics with Condition)
	ClinVar: CES2
Phenotype	MGI: CES2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: CES2

Mutations for CES2

* 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 CES2 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
CA427622	CES2	23	324	16	66978239	66978540	CES2	323	671	16	66976615	66977943
BG036772	CES2	6	151	16	66968352	66968497	CCDC92	149	538	12	124427894	124457214
AA368402	PTTG1IP	1	96	21	46270164	46270259	CES2	93	183	16	66968737	66968827
AW955878	PTTG1IP	1	96	21	46270164	46270259	CES2	93	617	16	66968737	66969262
CN478636	CES2	12	154	16	66978857	66978999	CES2	146	450	16	66977905	66978209
AW882114	ECE1	15	189	1	21544849	21545023	CES2	187	330	16	66978598	66978741

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr16:66974489-66974489	p.S300L	3
chr16:66975531-66975531	p.F410F	3
chr16:66974389-66974389	p.A267T	3
chr16:66972053-66972053	p.A128T	2
chr16:66976111-66976111	p.S478F	2
chr16:66974142-66974142	p.H211H	2
chr16:66974153-66974153	p.L215H	2
chr16:66975693-66975693	p.Q424R	2
chr16:66974180-66974180	p.D224G	2
chr16:66974398-66974398	p.R270C	2

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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	1		4			9		3			2	1				8	8		4
# mutation	2	1		4			9		3			2	1				8	8		4
nonsynonymous SNV	2	1		2			7		2			1					4	6		1
synonymous SNV				2			2		1			1	1				4	2		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
chr16:66974398	p.R270C,CES2	2
chr16:66975531	p.F410F,CES2	2
chr16:66975486	p.L22P,CES2	1
chr16:66972087	p.A267T,CES2	1
chr16:66977823	p.G459E,CES2	1
chr16:66974469	p.P24A,CES2	1
chr16:66972139	p.P464P,CES2	1
chr16:66974489	p.P43Q,CES2	1
chr16:66975679	p.A293A,CES2	1
chr16:66973125	p.A476A,CES2	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 CES2 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 CES2

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


ATP6V0D1,BBS2,C16orf70,CES2,COG8,EDC4,ELMO3, FAM65A,FBXO31,FUK,GAS8,GFOD2,KATNB1,IST1, MLYCD,PRMT7,PSKH1,RANBP10,TK2,TANGO6,VPS4A	ACTR1B,BAP1,BAG6,C3orf18,CAMTA2,CES2,COG4, DNAJC11,EVI5L,EXOC3,NLRX1,NOL3,NUDCD3,PRDX2, RMND5B,RPTOR,TBC1D17,VPS4A,WBSCR16,ZER1,ZFAND3

ASTE1,TMEM253,CALCB,CES2,CHP2,CLDN15,CLDN22, CYP7A1,DHRS11,HNF4A,INSC,OSTalpha,PRSS8,RAB22A, SERPINE3,SLC7A9,SULT1A2,TM6SF2,TMEM150B,TMEM229A,TMEM82	SOWAHA,CDHR5,CES2,DHRS11,GDPD2,HNF1A,INPP5J, IYD,KIAA2013,MEP1A,MOGAT2,MYO1A,NGEF,PIGS, POR,RAB17,SLC22A4,SLC39A5,SLC3A1,USH1C,VIL1

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 CES2

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
DB00951	carboxylesterase 2	approved	Isoniazid
DB06209	carboxylesterase 2	approved; investigational	Prasugrel
DB01101	carboxylesterase 2	approved; investigational	Capecitabine
DB00544	carboxylesterase 2	approved	Fluorouracil
DB00762	carboxylesterase 2	approved; investigational	Irinotecan

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Cross referenced IDs for CES2

* 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