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 ALDH3A2

Basic gene info.	Gene symbol	ALDH3A2
	Gene name	aldehyde dehydrogenase 3 family, member A2
	Synonyms	ALDH10\|FALDH\|SLS
	Cytomap	UCSC genome browser: 17p11.2
	Genomic location	chr17 :19552063-19580904
	Type of gene	protein-coding
	RefGenes	NM_000382.2, NM_001031806.1,
	Ensembl id	ENSG00000072210
	Description	aldehyde dehydrogenase 10aldehyde dehydrogenase family 3 member A2fatty aldehyde dehydrogenasemicrosomal aldehyde dehydrogenase
	Modification date	20141207
dbXrefs	MIM : 609523
	HGNC : HGNC
	Ensembl : ENSG00000072210
	HPRD : 07188
	Vega : OTTHUMG00000059471
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALDH3A2
	BioGPS: 224
	Gene Expression Atlas: ENSG00000072210
	The Human Protein Atlas: ENSG00000072210
Pathway	NCI Pathway Interaction Database: ALDH3A2
	KEGG: ALDH3A2
	REACTOME: ALDH3A2
	ConsensusPathDB
	Pathway Commons: ALDH3A2
Metabolism	MetaCyc: ALDH3A2
	HUMANCyc: ALDH3A2
Regulation	Ensembl's Regulation: ENSG00000072210
	miRBase: chr17 :19,552,063-19,580,904
	TargetScan: NM_000382
	cisRED: ENSG00000072210
Context	iHOP: ALDH3A2
	cancer metabolism search in PubMed: ALDH3A2
	UCL Cancer Institute: ALDH3A2
Assigned class in ccmGDB	C

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Phenotypic Information for ALDH3A2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ALDH3A2
	Familial Cancer Database: ALDH3A2

* 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
Orphanet
Disease	KEGG Disease: ALDH3A2
	MedGen: ALDH3A2 (Human Medical Genetics with Condition)
	ClinVar: ALDH3A2
Phenotype	MGI: ALDH3A2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALDH3A2

Mutations for ALDH3A2

* 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

* 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
haematopoietic_and_lymphoid_tissue	ALDH3A2	chr17	19562503	19562503	ALDH3A2	chr17	19562503	19562503
pancreas	ALDH3A2	chr17	19574460	19574480	MYO1D	chr17	30849010	30849030
pancreas	ALDH3A2	chr17	19577237	19577257	B9D1	chr17	19271497	19271517

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 ALDH3A2 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
BF854270	NEAT1	8	253	11	65194439	65194684	ALDH3A2	245	444	17	19566989	19567188
BF845221	ALDH3A2	14	299	17	19558741	19559029	SMC1A	296	578	X	53438739	53439114
AV652827	ALDH3A2	1	534	17	19569307	19569840	LOC646214	530	727	15	21933563	21933818
AI769187	ATP1B2	1	112	17	7560293	7560404	ALDH3A2	108	276	17	19552135	19552303

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=12)

Stat. for Deletions (# total SNVs=1)	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
chr17:19575149-19575149	p.P441P	3
chr17:19568332-19568332	p.T393T	3
chr17:19555901-19555901	p.T143fs*13	2
chr17:19568264-19568264	p.I371V	2
chr17:19575075-19575075	p.D417H	2
chr17:19568265-19568265	p.I371T	2
chr17:19564539-19564539	p.I300L	2
chr17:19564573-19564573	p.R311H	2
chr17:19559759-19559759	p.T184T	2
chr17:19559761-19559761	p.G185V	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				13			1		2	2		4		3		1	2	5		4
# mutation				11			1		2	2		4		3		1	2	5		5
nonsynonymous SNV				9					2	2		3		2			2	5		3
synonymous SNV				2			1					1		1		1				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
chr17:19575149	p.P441P,ALDH3A2	3
chr17:19568264	p.I371V,ALDH3A2	2
chr17:19568265	p.I371T,ALDH3A2	2
chr17:19575102	p.T184T,ALDH3A2	1
chr17:19559709	p.Q422Q,ALDH3A2	1
chr17:19575133	p.D219Y,ALDH3A2	1
chr17:19559734	p.P424H,ALDH3A2	1
chr17:19568270	p.T230A,ALDH3A2	1
chr17:19575148	p.L426V,ALDH3A2	1
chr17:19559758	p.R311H,ALDH3A2	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 ALDH3A2 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 ALDH3A2

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


ACADSB,AKAP10,ALDH3A2,ZFAND4,ANXA9,AP1AR,B9D1, COQ7,EPN2,FLNB,GIN1,KRT37,PEX12,SFXN2, SGK3,SIAH2,SLC27A2,SNX24,STC2,SYBU,ULK2	ALDH3A2,CLMP,ASPH,ATP9A,BHMT2,BTD,MTURN, CCDC69,DHDDS,DMGDH,FOXN3,MRAS,PLXNA4,PYGL, SNN,SORBS1,TK2,TLN2,TNS1,TTC7B,VKORC1L1

AKAP10,ALDH3A1,ALDH3A2,B9D1,CYSTM1,CLDN7,SPECC1, DHRS7B,EPN2,GCGR,MAPK7,MED11,MPDU1,PLIN5, SNORA11E,TMEM102,TMEM11,TNK1,TRIM16,ULK2,USP22	ABHD5,ACOT4,ADH1C,AGMAT,ALDH3A2,APMAP,C2orf47, DNAJC25,ETFA,FAM45A,FDX1,GCLM,KCNV1,ME2, MTCH2,PEX11A,PHYH,PITX2,RPP25,SLC27A2,TMEM139

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 ALDH3A2

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
DB00157	aldehyde dehydrogenase 3 family, member A2	approved; nutraceutical	NADH

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Cross referenced IDs for ALDH3A2

* 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