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 ASPA

Basic gene info.	Gene symbol	ASPA
	Gene name	aspartoacylase
	Synonyms	ACY2\|ASP
	Cytomap	UCSC genome browser: 17p13.3
	Genomic location	chr17 :3377403-3402700
	Type of gene	protein-coding
	RefGenes	NM_000049.2, NM_001128085.1,
	Ensembl id	ENSG00000108381
	Description	ACY-2aminoacylase 2aminoacylase-2
	Modification date	20141219
dbXrefs	MIM : 608034
	HGNC : HGNC
	HPRD : 02033
Protein	UniProt: P45381 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ASPA
	BioGPS: 443
	Gene Expression Atlas: ENSG00000108381
	The Human Protein Atlas: ENSG00000108381
Pathway	NCI Pathway Interaction Database: ASPA
	KEGG: ASPA
	REACTOME: ASPA
	ConsensusPathDB
	Pathway Commons: ASPA
Metabolism	MetaCyc: ASPA
	HUMANCyc: ASPA
Regulation	Ensembl's Regulation: ENSG00000108381
	miRBase: chr17 :3,377,403-3,402,700
	TargetScan: NM_000049
	cisRED: ENSG00000108381
Context	iHOP: ASPA
	cancer metabolism search in PubMed: ASPA
	UCL Cancer Institute: ASPA
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of ASPA in cancer cell metabolism	1. 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 2. Tsen AR, Long PM, Driscoll HE, Davies MT, Teasdale BA, et al. (2014) Triacetin-based acetate supplementation as a chemotherapeutic adjuvant therapy in glioma. Int J Cancer 134: 1300-1310. doi: 10.1002/ijc.28465. pmid: 3947395. go to article 3. Long PM, Moffett JR, Namboodiri AM, Viapiano MS, Lawler SE, et al. (2013) N-acetylaspartate (NAA) and N-acetylaspartylglutamate (NAAG) promote growth and inhibit differentiation of glioma stem-like cells. J Biol Chem 288: 26188-26200. doi: 10.1074/jbc.M113.487553. pmid: 3764823. go to article

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

Cancer Description
Cancer	CGAP: ASPA
	Familial Cancer Database: ASPA

* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM KEGG_HISTIDINE_METABOLISM

Others
OMIM	271900; phenotype. 608034; gene.
Orphanet	314911; Severe Canavan disease. 314918; Mild Canavan disease.
Disease	KEGG Disease: ASPA
	MedGen: ASPA (Human Medical Genetics with Condition)
	ClinVar: ASPA
Phenotype	MGI: ASPA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ASPA

Mutations for ASPA

* 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	ASPA	chr17	3383932	3383952	ASPA	chr17	3388191	3388211

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 ASPA 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

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=31)	Stat. for Synonymous SNVs (# total SNVs=6)

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
chr17:3402365-3402365	p.R309C	3
chr17:3392582-3392582	p.Q194K	2
chr17:3386854-3386854	p.A165V	2
chr17:3392563-3392563	p.L187L	1
chr17:3379514-3379514	p.H21D	1
chr17:3397735-3397735	p.I242I	1
chr17:3385047-3385047	p.E129D	1
chr17:3402370-3402370	p.C310*	1
chr17:3379604-3379605	p.I52_T53insI	1
chr17:3397738-3397738	p.I243I	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	2			8			1		1			4	1	1		1	4	2		5
# mutation	2			8			1		1			4	1	1		1	4	2		5
nonsynonymous SNV	2			7			1		1			2		1			4	1		4
synonymous SNV				1								2	1			1		1		1

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
chr17:3402365	p.A165V,ASPA	2
chr17:3386854	p.R309C,ASPA	2
chr17:3397735	p.D104G,ASPA	1
chr17:3379649	p.K224E,ASPA	1
chr17:3386871	p.I112M,ASPA	1
chr17:3402247	p.V229V,ASPA	1
chr17:3384912	p.L115I,ASPA	1
chr17:3392558	p.P232S,ASPA	1
chr17:3402272	p.C124F,ASPA	1
chr17:3384971	p.I242I,ASPA	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 ASPA 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 ASPA

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


ABCA8,ADH1B,ADIPOQ,AOC3,AQP7,ASPA,CDH5, CHRDL1,CXorf36,EBF1,ERG,FHL1,GPD1,ITIH5, KCNIP2,LDB2,LHFP,NPR1,PLIN1,PTPRB,TNS1	ABCC9,ANKRD40,APOL6,ARHGEF7,ASPA,DIAPH2,DMGDH, RMDN1,HSDL2,MAP7D3,NRP1,PALMD,PPP2R1B,SEC23A, SH3GLB1,SORT1,TSPAN3,TTC7B,UGP2,YWHAG,ZEB1

ABCA6,ABCA8,ABCA9,ABI3BP,ADH1B,ASPA,BHMT2, CDO1,EBF1,EXTL1,FHL1,GPIHBP1,GPR146,ITIH5, LIFR,LOC339524,MAPK10,PALMD,PDE1B,PTGER3,SEMA3G	AIG1,ARHGDIG,ASPA,CYBRD1,DEFA5,DEFA6,DFNA5, GATA5,HOXC8,HOXC9,KHK,LRAT,MRO,OAT, OTC,PHYHIPL,PRSS1,REG3A,RHOBTB2,SFRP5,PRSS3P2

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 ASPA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA25055; -.
Organism-specific databases	CTD	443; -.

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
DB00128	aspartoacylase	approved; nutraceutical	L-Aspartic Acid

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Cross referenced IDs for ASPA

* 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