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 ACP2

Basic gene info.	Gene symbol	ACP2
	Gene name	acid phosphatase 2, lysosomal
	Synonyms	LAP
	Cytomap	UCSC genome browser: 11p11.2\|11p12-p11
	Genomic location	chr11 :47260852-47270457
	Type of gene	protein-coding
	RefGenes	NM_001302489.1, NM_001302490.1,NM_001302491.1,NM_001302492.1,NM_001610.3, NM_001131064.1,
	Ensembl id	ENSG00000134575
	Description	lysosomal acid phosphatase
	Modification date	20141207
dbXrefs	MIM : 171650
	HGNC : HGNC
	Ensembl : ENSG00000134575
	HPRD : 01375
	Vega : OTTHUMG00000166949
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ACP2
	BioGPS: 53
	Gene Expression Atlas: ENSG00000134575
	The Human Protein Atlas: ENSG00000134575
Pathway	NCI Pathway Interaction Database: ACP2
	KEGG: ACP2
	REACTOME: ACP2
	ConsensusPathDB
	Pathway Commons: ACP2
Metabolism	MetaCyc: ACP2
	HUMANCyc: ACP2
Regulation	Ensembl's Regulation: ENSG00000134575
	miRBase: chr11 :47,260,852-47,270,457
	TargetScan: NM_001302489
	cisRED: ENSG00000134575
Context	iHOP: ACP2
	cancer metabolism search in PubMed: ACP2
	UCL Cancer Institute: ACP2
Assigned class in ccmGDB	C

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Phenotypic Information for ACP2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ACP2
	Familial Cancer Database: ACP2

* 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_RIBOFLAVIN_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: ACP2
	MedGen: ACP2 (Human Medical Genetics with Condition)
	ClinVar: ACP2
Phenotype	MGI: ACP2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ACP2

Mutations for ACP2

* 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
pancreas	ACP2	chr11	47263375	47263395	DDB2	chr11	47242257	47242277

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 ACP2 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
DA582448	ACP2	96	438	11	47267353	47270356	MRVI1-AS1	428	540	11	10590053	10590165
AK097626	ACP2	1	1919	11	47268438	47270356	KIRREL3	1912	2067	11	126792984	126793353

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=7)

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
chr11:47264443-47264443	p.F323F	2
chr11:47269233-47269233	p.R86C	2
chr11:47269678-47269678	p.R41C	2
chr11:47266897-47266897	p.L200L	2
chr11:47261788-47261788	p.A384V	2
chr11:47267093-47267093	p.R161C	2
chr11:47266388-47266388	p.A224T	1
chr11:47267247-47267247	p.I146V	1
chr11:47264624-47264624	p.E303K	1
chr11:47269242-47269242	p.L83V	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	1			8			1		1			2	1	1			4	4		3
# mutation	1			8			1		1			2	1	1			4	4		3
nonsynonymous SNV				7			1		1			2	1	1			1	2		2
synonymous SNV	1			1													3	2		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
chr11:47264815	p.W204R	1
chr11:47267287	p.E201E	1
chr11:47264838	p.G194V	1
chr11:47267305	p.R181Q	1
chr11:47264856	p.R414H	1
chr11:47267352	p.S180F	1
chr11:47261698	p.V402I	1
chr11:47266884	p.R161C	1
chr11:47267355	p.Q352Q	1
chr11:47261735	p.I146V,ACP2	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 ACP2 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 ACP2

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


ACP2,ARFGAP2,C1QA,DDB2,FUCA1,GRN,IFI30, LMAN2,MPDU1,NDUFS3,NR1H3,PACSIN3,PEX16,PSMB10, PSMC3,PSME1,PSME2,SIL1,TYMP,TYROBP,VAMP8	ABHD12,ACP2,ALDH3B1,AP2S1,ARPC1B,ATOX1,C1orf85, CSTB,CTSD,CTSZ,FCGRT,GRN,HPCAL1,NAGPA, PLD3,PSAP,LAMTOR2,SIL1,SLC8B1,SMPD1,TYROBP

ABI3,ACP2,AIF1,C10orf54,C1QA,C1QB,C1QC, CTSD,FCGR1B,GNAI2,IFI30,IL4I1,ITGB2,LAIR1, MGAT1,OSCAR,PLD3,SLAMF8,SLC15A3,SPI1,TYROBP	ACP2,CTSZ,ESPN,FAM83F,HECTD3,ITGA3,LASP1, MAPK3,PARP12,PLEKHG6,PRKCD,PRKCZ,PRSS8,SESN2, SLC9A3R1,SPINT1,SRC,TNIP1,TOM1,TRIM14,VPS33B

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 ACP2

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
DB01033	acid phosphatase 2, lysosomal	approved	Mercaptopurine
DB00563	acid phosphatase 2, lysosomal	approved	Methotrexate

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Cross referenced IDs for ACP2

* 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