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 ALDH18A1

Basic gene info.	Gene symbol	ALDH18A1
	Gene name	aldehyde dehydrogenase 18 family, member A1
	Synonyms	ARCL3A\|GSAS\|P5CS\|PYCS
	Cytomap	UCSC genome browser: 10q24.3
	Genomic location	chr10 :97365685-97416567
	Type of gene	protein-coding
	RefGenes	NM_001017423.1, NM_002860.3,
	Ensembl id	ENSG00000059573
	Description	aldehyde dehydrogenase family 18 member A1delta-1-pyrroline-5-carboxylate synthasedelta-1-pyrroline-5-carboxylate synthetasedelta1-pyrroline-5-carboxlate synthetasepyrroline-5-carboxylate synthetase (glutamate gamma-semialdehyde synthetase)
	Modification date	20141211
dbXrefs	MIM : 138250
	HGNC : HGNC
	Ensembl : ENSG00000059573
	HPRD : 00696
	Vega : OTTHUMG00000018815
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ALDH18A1
	BioGPS: 5832
	Gene Expression Atlas: ENSG00000059573
	The Human Protein Atlas: ENSG00000059573
Pathway	NCI Pathway Interaction Database: ALDH18A1
	KEGG: ALDH18A1
	REACTOME: ALDH18A1
	ConsensusPathDB
	Pathway Commons: ALDH18A1
Metabolism	MetaCyc: ALDH18A1
	HUMANCyc: ALDH18A1
Regulation	Ensembl's Regulation: ENSG00000059573
	miRBase: chr10 :97,365,685-97,416,567
	TargetScan: NM_001017423
	cisRED: ENSG00000059573
Context	iHOP: ALDH18A1
	cancer metabolism search in PubMed: ALDH18A1
	UCL Cancer Institute: ALDH18A1
Assigned class in ccmGDB	C

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Phenotypic Information for ALDH18A1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ALDH18A1
	Familial Cancer Database: ALDH18A1

* 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_ARGININE_AND_PROLINE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

Others
OMIM
Orphanet
Disease	KEGG Disease: ALDH18A1
	MedGen: ALDH18A1 (Human Medical Genetics with Condition)
	ClinVar: ALDH18A1
Phenotype	MGI: ALDH18A1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ALDH18A1

Mutations for ALDH18A1

* 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	ALDH18A1	chr10	97378419	97378439	ALDH18A1	chr10	97378144	97378164

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 ALDH18A1 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
BX503218	ALDH18A1	1	264	10	97385120	97387295	ZNF271	259	488	18	32888363	32888589
EY198528	ALDH18A1	1	241	10	97366159	97366399	CALCOCO2	238	406	17	46937745	46940272
BG959752	ALDH18A1	6	81	10	97373570	97373750	HGSNAT	76	153	8	43056307	43056388
BP341719	ALDH18A1	1	463	10	97371083	97416468	ALDH18A1	454	579	10	97402862	97413070

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=43)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=1)	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
chr10:97397115-97397115	p.R128C	3
chr10:97402861-97402861	p.R64H	2
chr10:97380889-97380889	p.R456C	2
chr10:97396856-97396856	p.A184A	2
chr10:97380890-97380890	p.L455L	2
chr10:97373858-97373858	p.I556V	2
chr10:97371130-97371130	p.R665*	2
chr10:97366663-97366663	p.A748A	2
chr10:97387287-97387287	p.G330G	2
chr10:97397089-97397089	p.S136S	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=4

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	1	2	1	13	1		2		4			3	4			1	4	7		7
# mutation	1	2	1	10	1		2		4			5	4			1	5	8		11
nonsynonymous SNV		2		6			2		2			1	4			1	4	5		7
synonymous SNV	1		1	4	1				2			4					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
chr10:97397115	p.R128C,ALDH18A1	4
chr10:97380888	p.I554V,ALDH18A1	2
chr10:97366665	p.A746T,ALDH18A1	2
chr10:97373858	p.R454H,ALDH18A1	2
chr10:97387227	p.G93W,ALDH18A1	1
chr10:97371060	p.R636S,ALDH18A1	1
chr10:97397084	p.G348G,ALDH18A1	1
chr10:97376261	p.L92V,ALDH18A1	1
chr10:97366548	p.L785I,ALDH18A1	1
chr10:97387287	p.I631I,ALDH18A1	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 ALDH18A1 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 ALDH18A1

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


ALDH18A1,CCNJ,CKAP4,CLDN2,COPB2,EIF4EBP2,ENTPD7, GLRX3,KDELR2,KDELR3,MORC4,PCBD1,PPA1,SAR1A, SPANXD,SUPV3L1,TAAR6,TCTN3,TM9SF3,UGT2B7,VPS26A	ALDH18A1,C2orf15,CANT1,CDH1,EPCAM,FKBP4,IGSF3, KIAA1324,KIAA1549,MYO5B,NIPSNAP1,PDIA4,PTK7,RCC2, SEC23B,SLC12A8,SMPDL3B,SPATS2,SYT7,TOM1L1,XPO5

A1CF,ALDH18A1,ATAD1,C10orf2,R3HCC1L,C10orf76,CCNJ, COX15,DNAJB12,DNMBP,FRAT2,IDE,NOLC1,PARG, PPRC1,RRP12,SLC11A2,TCTN3,TM9SF3,WAPAL,ZDHHC16	ACOX1,AGPAT3,ALDH18A1,APLP2,ATP9A,ERBB3,LAMB3, MAST2,MGAT4A,MYO1D,NDRG1,PAG1,PSEN1,PTPRF, RETSAT,RMND5A,RNF103,SLC41A2,SORL1,SOS2,TRHDE

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 ALDH18A1

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
DB00142	aldehyde dehydrogenase 18 family, member A1	approved; nutraceutical	L-Glutamic Acid

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Cross referenced IDs for ALDH18A1

* 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