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 ALDH2

Basic gene info.	Gene symbol	ALDH2
	Gene name	aldehyde dehydrogenase 2 family (mitochondrial)
	Synonyms	ALDH-E2\|ALDHI\|ALDM
	Cytomap	UCSC genome browser: 12q24.2
	Genomic location	chr12 :112204690-112247789
	Type of gene	protein-coding
	RefGenes	NM_000690.3, NM_001204889.1,
	Ensembl id	ENSG00000111275
	Description	ALDH class 2acetaldehyde dehydrogenase 2aldehyde dehydrogenase, mitochondrialliver mitochondrial ALDHnucleus-encoded mitochondrial aldehyde dehydrogenase 2
	Modification date	20141222
dbXrefs	MIM : 100650
	HGNC : HGNC
	Ensembl : ENSG00000111275
	HPRD : 00003
	Vega : OTTHUMG00000169603
Protein	UniProt: P05091 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALDH2
	BioGPS: 217
	Gene Expression Atlas: ENSG00000111275
	The Human Protein Atlas: ENSG00000111275
Pathway	NCI Pathway Interaction Database: ALDH2
	KEGG: ALDH2
	REACTOME: ALDH2
	ConsensusPathDB
	Pathway Commons: ALDH2
Metabolism	MetaCyc: ALDH2
	HUMANCyc: ALDH2
Regulation	Ensembl's Regulation: ENSG00000111275
	miRBase: chr12 :112,204,690-112,247,789
	TargetScan: NM_000690
	cisRED: ENSG00000111275
Context	iHOP: ALDH2
	cancer metabolism search in PubMed: ALDH2
	UCL Cancer Institute: ALDH2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ALDH2 in cancer cell metabolism	1. Hakenewerth AM, Millikan RC, Rusyn I, Herring AH, North KE, et al. (2011) Joint effects of alcohol consumption and polymorphisms in alcohol and oxidative stress metabolism genes on risk of head and neck cancer. Cancer Epidemiol Biomarkers Prev 20: 2438-2449. doi: 10.1158/1055-9965.EPI-11-0649. pmid: 3210881. go to article 2. Oh HR, An CH, Yoo NJ, Lee SH (2014) Somatic mutations of amino acid metabolism-related genes in gastric and colorectal cancers and their regional heterogeneity--a short report. Cell Oncol (Dordr) 37: 455-461. doi: 10.1007/s13402-014-0209-1. go to article 3. Tsai ST, Wong TY, Ou CY, Fang SY, Chen KC, et al. (2014) The interplay between alcohol consumption, oral hygiene, ALDH2 and ADH1B in the risk of head and neck cancer. Int J Cancer 135: 2424-2436. doi: 10.1002/ijc.28885. go to article 4. Jin S, Chen J, Chen L, Histen G, Lin Z, et al. (2015) ALDH2(E487K) mutation increases protein turnover and promotes murine hepatocarcinogenesis. Proc Natl Acad Sci U S A. doi: 10.1073/pnas.1510757112. go to article

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Phenotypic Information for ALDH2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ALDH2
	Familial Cancer Database: ALDH2

* 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_GLYCOLYSIS_GLUCONEOGENESIS KEGG_ASCORBATE_AND_ALDARATE_METABOLISM KEGG_FATTY_ACID_METABOLISM KEGG_ARGININE_AND_PROLINE_METABOLISM KEGG_HISTIDINE_METABOLISM KEGG_TRYPTOPHAN_METABOLISM KEGG_BETA_ALANINE_METABOLISM KEGG_GLYCEROLIPID_METABOLISM KEGG_PYRUVATE_METABOLISM KEGG_PROPANOATE_METABOLISM KEGG_BUTANOATE_METABOLISM

Others
OMIM	100650; gene+phenotype. 610251; phenotype.
Orphanet
Disease	KEGG Disease: ALDH2
	MedGen: ALDH2 (Human Medical Genetics with Condition)
	ClinVar: ALDH2
Phenotype	MGI: ALDH2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALDH2

Mutations for ALDH2

* 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
ovary	ALDH2	chr12	112246575	112246595		chr12	112249094	112249114

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 ALDH2 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
S80262	RPSAP52	1	184	12	66219118	66232351	ALDH2	182	410	12	112247346	112247574
CA309127	ALDH2	17	481	12	112241751	112247784	KCNE1	471	744	21	35819819	35820094
AI907073	ALDH2	61	282	12	112230461	112235978	ALDH2	273	475	12	112236012	112237886

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=7

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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=6)

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
chr12:112228251-112228251	p.L189P	6
chr12:112235926-112235926	p.T376T	3
chr12:112221067-112221067	p.A109T	2
chr12:112237741-112237741	p.F427S	2
chr12:112219760-112219760	p.R51R	2
chr12:112227732-112227732	p.I182I	2
chr12:112237856-112237856	p.A465A	2
chr12:112235944-112235944	p.A382A	2
chr12:112221025-112221025	p.R95C	1
chr12:112229927-112229927	p.L286L	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=6

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				11			1		2	2		2	2	1			12	3		5
# mutation				6			1		2	2		2	2	1			10	3		5
nonsynonymous SNV				6			1		2	2		1	2				3	3		3
synonymous SNV												1		1			7			2

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
chr12:112228251	p.L142P,ALDH2	6
chr12:112219760	p.R51R,ALDH2	2
chr12:112237856	p.A418A,ALDH2	2
chr12:112223073	p.K336N,ALDH2	1
chr12:112229161	p.L142L,ALDH2	1
chr12:112237755	p.A345V,ALDH2	1
chr12:112223124	p.M144V,ALDH2	1
chr12:112229871	p.E385K,ALDH2	1
chr12:112237855	p.P151S,ALDH2	1
chr12:112227678	p.A418V,ALDH2	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 ALDH2 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 ALDH2

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


ACSM5,ADH1B,ADIPOQ,ALDH2,AOC3,AQP7,C14orf180, CEBPA,CIDEC,GIMAP1,GPD1,GPR146,KCNIP2,LIPE, LOC283392,NR1H3,PLIN1,SLC19A3,SLC8B1,TMEM132C,TMEM37	ACO1,ALDH2,AQP7,FAM213A,CALB2,CIDEC,FBXO27, GPD1,GYG2,HEPACAM,HEPN1,LIPE,NPR1,PJA1, PLA2G16,PLIN1,RDH5,TMEM132C,TUSC5,TYRO3,VTI1B

AACS,ACADS,ACOT11,ADH6,ALDH2,C10orf99,C11orf49, EPS8L3,FAM109A,GGT6,MAPKAPK5,MCCC2,MMAB,MVK, PRDX5,PRR13,SCARB1,SUCLG2,SUOX,TMEM53,TST	ABHD5,ACOX1,ALDH2,ANO10,APLP2,ATP1B1,LINC00483, SUGCT,CAST,RHOV___CHP1,ETFDH,GAREM,GNG12,MARVELD3, RNF103,SLC41A2,SMAP1,SPPL2A,TGFA,UGT1A10,VDAC1

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 ALDH2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P05091; -.
Chemistry	ChEMBL	CHEMBL1935; -.
Chemistry	GuidetoPHARMACOLOGY	2595; -.
Organism-specific databases	PharmGKB	PA24696; -.
Organism-specific databases	CTD	217; -.

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
DB00157	aldehyde dehydrogenase 2 family (mitochondrial)	approved; nutraceutical	NADH
DB00536	aldehyde dehydrogenase 2 family (mitochondrial)	approved	Guanidine
DB00822	aldehyde dehydrogenase 2 family (mitochondrial)	approved	Disulfiram
DB01907	aldehyde dehydrogenase 2 family (mitochondrial)	experimental	Nicotinamide-Adenine-Dinucleotide
DB02115	aldehyde dehydrogenase 2 family (mitochondrial)	experimental	Daidzin
DB04381	aldehyde dehydrogenase 2 family (mitochondrial)	experimental	Crotonaldehyde
DB00325	aldehyde dehydrogenase 2 family (mitochondrial)	approved	Nitroprusside
DB00727	aldehyde dehydrogenase 2 family (mitochondrial)	approved; investigational	Nitroglycerin
DB00898	aldehyde dehydrogenase 2 family (mitochondrial)	approved	Ethanol

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Cross referenced IDs for ALDH2

* 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