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 ACHE

Basic gene info.	Gene symbol	ACHE
	Gene name	acetylcholinesterase (Yt blood group)
	Synonyms	ACEE\|ARACHE\|N-ACHE\|YT
	Cytomap	UCSC genome browser: 7q22
	Genomic location	chr7 :100487614-100493541
	Type of gene	protein-coding
	RefGenes	NM_000665.4, NM_001282449.1,NM_001302621.1,NM_001302622.1,NM_015831.2,
	Ensembl id	ENSG00000087085
	Description	Yt blood groupacetylcholinesteraseapoptosis-related acetylcholinesterase
	Modification date	20141207
dbXrefs	MIM : 100740
	HGNC : HGNC
	Ensembl : ENSG00000087085
	HPRD : 00010
	Vega : OTTHUMG00000157033
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACHE
	BioGPS: 43
	Gene Expression Atlas: ENSG00000087085
	The Human Protein Atlas: ENSG00000087085
Pathway	NCI Pathway Interaction Database: ACHE
	KEGG: ACHE
	REACTOME: ACHE
	ConsensusPathDB
	Pathway Commons: ACHE
Metabolism	MetaCyc: ACHE
	HUMANCyc: ACHE
Regulation	Ensembl's Regulation: ENSG00000087085
	miRBase: chr7 :100,487,614-100,493,541
	TargetScan: NM_000665
	cisRED: ENSG00000087085
Context	iHOP: ACHE
	cancer metabolism search in PubMed: ACHE
	UCL Cancer Institute: ACHE
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: ACHE
	Familial Cancer Database: ACHE

* 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: ACHE
	MedGen: ACHE (Human Medical Genetics with Condition)
	ClinVar: ACHE
Phenotype	MGI: ACHE (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ACHE

Mutations for ACHE

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	ACHE	chr7	100489340	100489360		chr15	83421902	83421922

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 ACHE related fusion information.

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

R96128

CDK6

92331061

92331104

ACHE

382

100490125

100490803

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=31)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr7:100490067-100490067	p.E481K	3
chr7:100491611-100491611	p.P81P	3
chr7:100491461-100491461	p.N131N	2
chr7:100491616-100491616	p.P80S	2
chr7:100490875-100490875	p.R327W	2
chr7:100490077-100490077	p.P477P	2
chr7:100491150-100491150	p.A235E	2
chr7:100488658-100488658	p.P592R	2
chr7:100488914-100488914	p.P533P	1
chr7:100490873-100490873	p.R327R	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	5		1	7	1		3					7	4		1		5	13		7
# mutation	6		1	7	1		3					7	4		1		5	14		7
nonsynonymous SNV	4			4			2					4	3		1		4	11		3
synonymous SNV	2		1	3	1		1					3	1				1	3		4

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
chr7:100491616	p.N131N,ACHE	2
chr7:100491048	p.E481K,ACHE	2
chr7:100491461	p.T269M,ACHE	2
chr7:100490067	p.P80S,ACHE	2
chr7:100488959	p.T497T,ACHE	1
chr7:100491167	p.R327R,ACHE	1
chr7:100490137	p.V176E,ACHE	1
chr7:100491577	p.G487G,ACHE	1
chr7:100490900	p.S324S,ACHE	1
chr7:100489998	p.I482V,ACHE	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 ACHE 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 ACHE

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


ACHE,ADAD2,BVES,TBC1D32,CASP8AP2,EPHB4,EPO, FABP7,HINT3,HSF2,LYRM2,MAP3K7,MDN1,RRAGD, SERINC1,SMPDL3A,STAG3,TRMT11,UBE2J1,UNCX,ZAN	RBFOX1,ACHE,ANKRD23,CACNG1,CALML6,CAPN3,CASQ1, DUSP26,FITM1,FLJ41941,KCNA7,MB,MYADML2,MYBPH, MYOM3,RYR1,TMEM38A,TNNI2,TRIM63,TRIM72,UCP3

ACHE,B3GALT4,LINC00520,C1orf94,CAPN11,CIDEC,CLDN23, CLTB,DHRS9,MYPN,PLAC8,RIOK3,RSAD2,SAMD9, SDCBP2,SI,TRANK1,TSPAN1,UGT1A4,UGT1A5,VSIG1	ACHE,C18orf8,CARS,CASP10,CDKN1A,CEACAM6,DIRC2, EHD1,GPRIN1,IL3RA,IRF9,MDK,MT2A,MUC13, MXD1,PLIN3,PPP4R1,RHOG,RIPK3,SAMD9,ZER1

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 ACHE

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
DB00122	acetylcholinesterase	approved; nutraceutical	Choline
DB00382	acetylcholinesterase	approved	Tacrine
DB00483	acetylcholinesterase	approved	Gallamine Triethiodide
DB00545	acetylcholinesterase	approved	Pyridostigmine
DB00674	acetylcholinesterase	approved	Galantamine
DB00677	acetylcholinesterase	approved	Isoflurophate
DB00733	acetylcholinesterase	approved	Pralidoxime
DB00805	acetylcholinesterase	approved	Minaprine
DB00843	acetylcholinesterase	approved	Donepezil
DB00944	acetylcholinesterase	approved	Demecarium
DB00981	acetylcholinesterase	approved	Physostigmine
DB00989	acetylcholinesterase	approved; investigational	Rivastigmine
DB01010	acetylcholinesterase	approved	Edrophonium
DB01122	acetylcholinesterase	approved	Ambenonium
DB01199	acetylcholinesterase	approved	Tubocurarine
DB01245	acetylcholinesterase	approved	Decamethonium
DB01364	acetylcholinesterase	approved	Ephedrine
DB01400	acetylcholinesterase	approved	Neostigmine
DB01805	acetylcholinesterase	experimental	Monoisopropylphosphorylserine
DB01928	acetylcholinesterase	experimental	Huperaine A
DB02166	acetylcholinesterase	experimental	Propidium
DB02226	acetylcholinesterase	experimental	3,8-Diamino-6-Phenyl-5-[6-[1-[2-[(1,2,3,4-Tetrahydro-9-Acridinyl)Amino]Ethyl]-1h-1,2,3-Triazol-4-Yl]Hexyl]-Phenanthridinium
DB02343	acetylcholinesterase	experimental	3,6,9,12,15-Pentaoxaheptadecane
DB02404	acetylcholinesterase	experimental	1-Deoxy-1-Thio-Heptaethylene Glycol
DB02673	acetylcholinesterase	experimental	(4ar,6s,8ar)-11-[8-(1,3-Dioxo-1,3-Dihydro-2h-Isoindol-2-Yl)Octyl]-6-Hydroxy-3-Methoxy-5,6,9,10-Tetrahydro-4ah-[1]Benzofuro[3a,3,2-Ef][2]Benzazepin-11-Ium
DB02825	acetylcholinesterase	experimental	Methylphosphonic Acid Ester Group
DB02845	acetylcholinesterase	experimental	Methylphosphinic Acid
DB03005	acetylcholinesterase	experimental	3,8-Diamino-6-Phenyl-5-[6-[1-[2-[(1,2,3,4-Tetrahydro-9-Acridinyl)Amino]Ethyl]-1h-1,2,3-Triazol-5-Yl]Hexyl]-Phenanthridinium
DB03128	acetylcholinesterase	experimental	Acetylcholine
DB03283	acetylcholinesterase	experimental	beta-L-fucose
DB03359	acetylcholinesterase	experimental	M-(N,N,N-Trimethylammonio)-2,2,2-Trifluoro-1,1-Dihydroxyethylbenzene
DB03740	acetylcholinesterase	experimental	2-(Acetylamino)-2-Deoxy-a-D-Glucopyranose
DB03814	acetylcholinesterase	experimental	2-(N-Morpholino)-Ethanesulfonic Acid
DB04021	acetylcholinesterase	experimental	MF268
DB04114	acetylcholinesterase	experimental	3-Chloro-9-Ethyl-6,7,8,9,10,11-Hexahydro-7,11-Methanocycloocta[B]Quinolin-12-Amine
DB04556	acetylcholinesterase	experimental	3-[(1s)-1-(Dimethylamino)Ethyl]Phenol
DB04614	acetylcholinesterase	experimental	(R)-tacrine(10)-hupyridone
DB04615	acetylcholinesterase	experimental	(S)-tacrine(10)-hupyridone
DB04616	acetylcholinesterase	experimental	TACRINE(8)-4-AMINOQUINOLINE
DB04617	acetylcholinesterase	experimental	(9S)-9-[(8-AMMONIOOCTYL)AMINO]-1,2,3,4,9,10-HEXAHYDROACRIDINIUM
DB07555	acetylcholinesterase	experimental	1-(2-nitrophenyl)-2,2,2-trifluoroethyl]-arsenocholine
DB07701	acetylcholinesterase	experimental	1-BENZYL-4-[(5,6-DIMETHOXY-1-INDANON-2-YL)METHYL]PIPERIDINE
DB07756	acetylcholinesterase	experimental	1-[3-({[(4-AMINO-5-FLUORO-2-METHYLQUINOLIN-3-YL)METHYL]THIO}METHYL)PHENYL]-2,2,2-TRIFLUOROETHANE-1,1-DIOL
DB07822	acetylcholinesterase	experimental	(1R)-1,2,2-TRIMETHYLPROPYL (S)-METHYLPHOSPHINATE
DB07846	acetylcholinesterase	experimental	1S,3AS,8AS-TRIMETHYL-1-OXIDO-1,2,3,3A,8,8A-HEXAHYDROPYRROLO[2,3-B]INDOL-5-YL 2-ETHYLPHENYLCARBAMATE
DB08167	acetylcholinesterase	experimental	3,7-BIS(DIMETHYLAMINO)PHENOTHIAZIN-5-IUM
DB08357	acetylcholinesterase	experimental	1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
DB08615	acetylcholinesterase	experimental	2-[4-(DIMETHYLAMINO)PHENYL]-6-HYDROXY-3-METHYL-1,3-BENZOTHIAZOL-3-IUM

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Cross referenced IDs for ACHE

* 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