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 CHAT

Basic gene info.	Gene symbol	CHAT
	Gene name	choline O-acetyltransferase
	Synonyms	CHOACTASE\|CMS1A\|CMS1A2
	Cytomap	UCSC genome browser: 10q11.2
	Genomic location	chr10 :50817140-50873150
	Type of gene	protein-coding
	RefGenes	NM_001142929.1, NM_001142933.1,NM_001142934.1,NM_020549.4,NM_020984.3, NM_020985.3,NM_020986.3,
	Ensembl id	ENSG00000070748
	Description	acetyl CoA:choline O-acetyltransferasecholine acetylase
	Modification date	20141219
dbXrefs	MIM : 118490
	HGNC : HGNC
	Ensembl : ENSG00000070748
	HPRD : 07510
	Vega : OTTHUMG00000018198
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_CHAT
	BioGPS: 1103
	Gene Expression Atlas: ENSG00000070748
	The Human Protein Atlas: ENSG00000070748
Pathway	NCI Pathway Interaction Database: CHAT
	KEGG: CHAT
	REACTOME: CHAT
	ConsensusPathDB
	Pathway Commons: CHAT
Metabolism	MetaCyc: CHAT
	HUMANCyc: CHAT
Regulation	Ensembl's Regulation: ENSG00000070748
	miRBase: chr10 :50,817,140-50,873,150
	TargetScan: NM_001142929
	cisRED: ENSG00000070748
Context	iHOP: CHAT
	cancer metabolism search in PubMed: CHAT
	UCL Cancer Institute: CHAT
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: CHAT
	Familial Cancer Database: CHAT

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

Mutations for CHAT

* 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

There's no inter-chromosomal structural variation.

- 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
breast	CHAT	chr10	50841766	50841766	CHAT	chr10	50850501	50850501
ovary	CHAT	chr10	50841487	50841507	CHAT	chr10	50843737	50843757

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 CHAT 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

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=81)	Stat. for Synonymous SNVs (# total SNVs=42)

Stat. for Deletions (# total SNVs=2)	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
chr10:50835688-50835688	p.R323H	5
chr10:50873054-50873054	p.E737K	3
chr10:50856579-50856579	p.C436*	3
chr10:50859978-50859978	p.G520G	3
chr10:50835781-50835781	p.T354R	3
chr10:50863468-50863468	p.R605C	2
chr10:50873015-50873015	p.L724L	2
chr10:50824633-50824633	p.P124P	2
chr10:50854636-50854636	p.S399S	2
chr10:50863149-50863149	p.R548Q	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=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	5	2		22	4		5		3			16	13	1		3	18	9	1	7
# mutation	5	2		23	4		5		3			16	13	1		3	19	10	1	11
nonsynonymous SNV	2	1		15	4		5		2			10	8			2	11	4		4
synonymous SNV	3	1		8					1			6	5	1		1	8	6	1	7

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
chr10:50859978	p.R205H,CHAT	3
chr10:50835688	p.G402G,CHAT	3
chr10:50856565	p.A439V,CHAT	2
chr10:50833529	p.S8S,CHAT	2
chr10:50863176	p.R314R,CHAT	2
chr10:50824639	p.P137S,CHAT	2
chr10:50828603	p.R427K,CHAT	1
chr10:50854677	p.S538Y,CHAT	1
chr10:50863479	p.I47S,CHAT	1
chr10:50835662	p.E611D,CHAT	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 CHAT 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 CHAT

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


C6orf132,CHAT,CLASP1,CT45A5,CTAG1B,LOC148824,NIFK, MRPS10,MSGN1,NARF,NDRG1,NXF2,PIWIL1,PRSS33, RIOK1,SIX2,SLC18A3,TMEM117,TSN,USP25,XPO5	NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA, NA,NA,NA,NA,NA,NA,NA

ASTN1,ATCAY,PIANP,CABP7,CHAT,CLVS2,DPYSL4, FAM196A,FUT9,HPCAL4,JPH4,KIAA1045,LRRC4B,RGAG4, SLC7A14,SSTR2,SYT4,SYT6,TCEAL5,TMEM59L,UNC80	ACAN,AWAT2,BMX,C20orf141,NCOR1P1,CCDC129,CHAT, CLEC4G,GPX5,KPRP,LCE2C,LPA,MEPE,CHODL-AS1, OR2D2,PGLYRP3,POU2F3,SH2D7,SNORA79,TRIM6-TRIM34,ZSWIM2

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 CHAT

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	choline O-acetyltransferase	approved; nutraceutical	Choline
DB01156	choline O-acetyltransferase	approved	Bupropion
DB03128	choline O-acetyltransferase	experimental	Acetylcholine
DB00843	choline O-acetyltransferase	approved	Donepezil

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Cross referenced IDs for CHAT

* 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