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 PLA2G6

Basic gene info.	Gene symbol	PLA2G6
	Gene name	phospholipase A2, group VI (cytosolic, calcium-independent)
	Synonyms	CaI-PLA2\|GVI\|INAD1\|IPLA2-VIA\|NBIA2\|NBIA2A\|NBIA2B\|PARK14\|PLA2\|PNPLA9\|iPLA2\|iPLA2beta
	Cytomap	UCSC genome browser: 22q13.1
	Genomic location	chr22 :38507501-38577761
	Type of gene	protein-coding
	RefGenes	NM_001004426.1, NM_001199562.1,NM_003560.2,
	Ensembl id	ENSG00000184381
	Description	85 kDa calcium-independent phospholipase A285/88 kDa calcium-independent phospholipase A2GVI PLA2calcium-independent phospholipase A2cytosolic, calcium-independent phospholipase A2group VI phospholipase A2iPLA2-betaintracellular membrane-associated
	Modification date	20141219
dbXrefs	MIM : 603604
	HGNC : HGNC
	Ensembl : ENSG00000184381
	HPRD : 04675
	Vega : OTTHUMG00000151246
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLA2G6
	BioGPS: 8398
	Gene Expression Atlas: ENSG00000184381
	The Human Protein Atlas: ENSG00000184381
Pathway	NCI Pathway Interaction Database: PLA2G6
	KEGG: PLA2G6
	REACTOME: PLA2G6
	ConsensusPathDB
	Pathway Commons: PLA2G6
Metabolism	MetaCyc: PLA2G6
	HUMANCyc: PLA2G6
Regulation	Ensembl's Regulation: ENSG00000184381
	miRBase: chr22 :38,507,501-38,577,761
	TargetScan: NM_001004426
	cisRED: ENSG00000184381
Context	iHOP: PLA2G6
	cancer metabolism search in PubMed: PLA2G6
	UCL Cancer Institute: PLA2G6
Assigned class in ccmGDB	C

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Phenotypic Information for PLA2G6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLA2G6
	Familial Cancer Database: PLA2G6

* 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 KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PLA2G6
	MedGen: PLA2G6 (Human Medical Genetics with Condition)
	ClinVar: PLA2G6
Phenotype	MGI: PLA2G6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLA2G6

Mutations for PLA2G6

* 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
skin	PLA2G6	chr22	38514511	38514511	TMEM184B	chr22	38643616	38643616

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 PLA2G6 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
CV375307	PLA2G6	2	99	22	38560565	38560662	CLTCL1	97	240	22	19228368	19228511
BQ300191	PLA2G6	10	229	22	38523889	38524110	MAP4	217	360	3	47917174	47917317
BF871762	SYT7	1	301	11	61300111	61300411	PLA2G6	291	373	22	38522251	38522333
CV375347	CLTCL1	83	226	22	19228368	19228511	PLA2G6	223	248	22	38560516	38560541

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=51)	Stat. for Synonymous SNVs (# total SNVs=14)

Stat. for Deletions (# total SNVs=2)	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
chr22:38539282-38539282	p.A147T	3
chr22:38524296-38524296	p.P443L	2
chr22:38531004-38531004	p.K295N	2
chr22:38512182-38512182	p.P593P	2
chr22:38508290-38508290	p.D767H	2
chr22:38536013-38536013	p.S258L	2
chr22:38509556-38509556	p.P714S	2
chr22:38536119-38536119	p.P223S	1
chr22:38509561-38509561	p.S712N	1
chr22:38541528-38541528	p.I114I	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	2		9	1		1	1	3			4	5	1			16	5		12
# mutation	2	2		9	1		1	2	3			4	5	1			17	5		13
nonsynonymous SNV	1	1		8	1		1	1	2			2	5	1			9	5		10
synonymous SNV	1	1		1				1	1			2					8			3

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
chr22:38536013	p.P660S,PLA2G6	2
chr22:38509556	p.S258L,PLA2G6	2
chr22:38509583	p.I248I,PLA2G6	1
chr22:38531068	p.P51S,PLA2G6	1
chr22:38516859	p.P539P,PLA2G6	1
chr22:38539144	p.A401A	1
chr22:38525475	p.N243K,PLA2G6	1
chr22:38565395	p.R39W,PLA2G6	1
chr22:38509647	p.D536D,PLA2G6	1
chr22:38516880	p.I393I,PLA2G6	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 PLA2G6 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 PLA2G6

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


LMNTD2,CAPN10,CCNL2,CDK10,CHKB-CPT1B,CPT1B,DENND6B, FLJ37453,GGA1,HDAC10,LOC338799,NEIL1,PILRB,PLA2G6, RNF215,SCNN1D,SELO,SFI1,TRMT2A,TUBGCP6,WASH7P	APBB3,ENTHD2,CCNL2,CSAD,ECHDC2,ENGASE,FAM193B, GIGYF1,HDAC6,HEMK1,HSF4,LENG8,LPIN3,MAN2C1, MYO15B,NSUN5P2,PILRB,PLA2G6,PNPLA7,TUBGCP6,WASH7P

ZNF436-AS1,CCNL2,CDK10,CDK5RAP3,CHKB-CPT1B,CROCCP2,CYP2D7, GGA1,HDAC10,LOC100131434,LOC91316,NOL12,PAN2,PI4KAP1, PICK1,PLA2G6,SFI1,SH2B1,TMEM175,TOP3B,TUBGCP6	ACAD10,VPS51___IFT46,LMNTD2,CCDC61,CNKSR1,COX19,DGKQ, DMAP1,FUK,HDAC10,HDAC6,MIB2,MYPOP,OPLAH, PLA2G6,PNPLA7,RNF44,SPPL2B,SPSB3,STK11,TPCN1

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 PLA2G6

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
DB01103	phospholipase A2, group VI (cytosolic, calcium-independent)	approved	Quinacrine

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Cross referenced IDs for PLA2G6

* 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