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 PLA2G2A

Basic gene info.	Gene symbol	PLA2G2A
	Gene name	phospholipase A2, group IIA (platelets, synovial fluid)
	Synonyms	MOM1\|PLA2\|PLA2B\|PLA2L\|PLA2S\|PLAS1\|sPLA2
	Cytomap	UCSC genome browser: 1p35
	Genomic location	chr1 :20301923-20306932
	Type of gene	protein-coding
	RefGenes	NM_000300.3, NM_001161727.1,NM_001161728.1,NM_001161729.1,
	Ensembl id	ENSG00000188257
	Description	GIIC sPLA2NPS-PLA2group IIA phospholipase A2non-pancreatic secretory phospholipase A2phosphatidylcholine 2-acylhydrolase 2Aphospholipase A2, membrane associated
	Modification date	20141222
dbXrefs	MIM : 172411
	HGNC : HGNC
	Ensembl : ENSG00000188257
	HPRD : 01397
	Vega : OTTHUMG00000002699
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLA2G2A
	BioGPS: 5320
	Gene Expression Atlas: ENSG00000188257
	The Human Protein Atlas: ENSG00000188257
Pathway	NCI Pathway Interaction Database: PLA2G2A
	KEGG: PLA2G2A
	REACTOME: PLA2G2A
	ConsensusPathDB
	Pathway Commons: PLA2G2A
Metabolism	MetaCyc: PLA2G2A
	HUMANCyc: PLA2G2A
Regulation	Ensembl's Regulation: ENSG00000188257
	miRBase: chr1 :20,301,923-20,306,932
	TargetScan: NM_000300
	cisRED: ENSG00000188257
Context	iHOP: PLA2G2A
	cancer metabolism search in PubMed: PLA2G2A
	UCL Cancer Institute: PLA2G2A
Assigned class in ccmGDB	C

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Phenotypic Information for PLA2G2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLA2G2A
	Familial Cancer Database: PLA2G2A

* 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_GLYCEROPHOSPHOLIPID_METABOLISM KEGG_ARACHIDONIC_ACID_METABOLISM KEGG_LINOLEIC_ACID_METABOLISM KEGG_ALPHA_LINOLENIC_ACID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PLA2G2A
	MedGen: PLA2G2A (Human Medical Genetics with Condition)
	ClinVar: PLA2G2A
Phenotype	MGI: PLA2G2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLA2G2A

Mutations for PLA2G2A

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLA2G2A 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
AI418780	PLA2G2A	1	66	1	20301929	20301994	MLLT4	62	455	6	168352373	168352766
BQ326672	GFRA1	1	115	10	117817772	117817887	PLA2G2A	105	337	1	20304519	20305012
BE646307	PLA2G2A	1	66	1	20301929	20301994	MLLT4	62	431	6	168352397	168352766
AI805196	PLA2G2A	1	66	1	20301929	20301994	MLLT4	62	431	6	168352397	168352766
CB050783	PLA2G2A	23	89	1	20301928	20301994	MLLT4	85	488	6	168352363	168352766

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=11)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr1:20302244-20302244	p.Y129H	2
chr1:20304926-20304926	p.Y44Y	2
chr1:20304874-20304874	p.R62C	1
chr1:20304905-20304905	p.G51G	1
chr1:20302255-20302255	p.Y125C	1
chr1:20304910-20304910	p.V50M	1
chr1:20302256-20302256	p.Y125N	1
chr1:20304920-20304920	p.C46C	1
chr1:20302318-20302318	p.R104K	1
chr1:20304510-20304510	p.C97F	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=1

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											5	1			1	3	1
# mutation	1											5	1			1	3	1
nonsynonymous SNV	1											5	1			1	2	1
synonymous SNV																	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
chr1:20302216	p.R138K,PLA2G2A	1
chr1:20305231	p.Y125N,PLA2G2A	1
chr1:20302256	p.R104K,PLA2G2A	1
chr1:20302318	p.C97F,PLA2G2A	1
chr1:20304510	p.S91L,PLA2G2A	1
chr1:20304528	p.C64R,PLA2G2A	1
chr1:20304610	p.C63S,PLA2G2A	1
chr1:20304613	p.R62C,PLA2G2A	1
chr1:20304874	p.S40R,PLA2G2A	1
chr1:20304940	p.G34E,PLA2G2A	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 PLA2G2A 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 PLA2G2A

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


AHSG,APOA1,APOB,CALCA,F11,G6PC,GLTPD2, GUCY2GP,HP,KNG1,LOC154822,PLA2G2A,PLA2G4A,SAA1, SERPINA7,SLC17A2,SLC22A2,SLC22A3,SLC2A2,SPP2,WNT1	ACSM2A,ACSM2B,AMN,APOC3,APOL4,TBATA,CHGA, CPO,DBH,ELFN1,NDRG4,ORM1,PDZD7,PHOX2B, PLA2G2A,PMM1,PQLC1,RASL10B,SNORA14A,ST8SIA3,TH

B3GNT7,CA9,MCU,DOC2B,ERO1L,FAM46A,FAM69C, HPSE,MTUS1,MUC1,PGAM1,PGC,PLA2G2A,PLAC8, PLK2,PPY,RARRES1,SLC6A14,TBC1D21,TNIP3,ZMYND15	APOL4,CD274,CXCL10,CXCL5,ERP27,FCGR1A,FCGR1B, FCGR1C,HAPLN3,IDO1,IL22,LOC400759,LYPD5,MMP1, PAQR9,PLA2G2A,PLA2G3,SOCS1,TNFSF13B,V

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 PLA2G2A

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
DB00328	phospholipase A2, group IIA (platelets, synovial fluid)	approved; investigational	Indomethacin
DB00586	phospholipase A2, group IIA (platelets, synovial fluid)	approved	Diclofenac
DB01955	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	1,4-Butanediol
DB02080	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	1-{2-[2-(2-Methoxyethoxy)Ethoxy]Ethoxy}-4-(1,1,3,3-Tetramethylbutyl)Benzene
DB02448	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	N-Tridecanoic Acid
DB02504	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	[3-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Propyl-]-Phosphonic Acid
DB02936	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	4-(1-Benzyl-3-Carbamoylmethyl-2-Methyl-1h-Indol-5-Yloxy)-Butyric Acid
DB03121	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	1-Benzyl-5-Methoxy-2-Methyl-1h-Indol-3-Yl)-Acetic Acid
DB03471	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	6-Phenyl-4(R)-(7-Phenyl-Heptanoylamino)-Hexanoic Acid
DB03784	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	Elaidoylamide
DB04112	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	1-Octadecyl-2-Acetamido-2-Deoxy-Sn-Glycerol-3-Phosphoethylmethyl Sulfide
DB04287	phospholipase A2, group IIA (platelets, synovial fluid)	experimental	(S)-5-(4-Benzyloxy-Phenyl)-4-(7-Phenyl-Heptanoylamino)-Pentanoic Acid
DB04786	phospholipase A2, group IIA (platelets, synovial fluid)	approved	Suramin
DB00435	phospholipase A2, group IIA (platelets, synovial fluid)	approved	Nitric Oxide
DB00482	phospholipase A2, group IIA (platelets, synovial fluid)	approved; investigational	Celecoxib

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Cross referenced IDs for PLA2G2A

* 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