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 PNPLA2

Basic gene info.	Gene symbol	PNPLA2
	Gene name	patatin-like phospholipase domain containing 2
	Synonyms	1110001C14Rik\|ATGL\|PEDF-R\|TTS-2.2\|TTS2\|iPLA2zeta
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :818900-825571
	Type of gene	protein-coding
	RefGenes	NM_020376.3,
	Ensembl id	ENSG00000177666
	Description	IPLA2-zetaTTS2.2adipose triglyceride lipasecalcium-independent phospholipase A2desnutrinpatatin-like phospholipase domain containing protein 2patatin-like phospholipase domain-containing protein 2pigment epithelium-derived factortransport-secretio
	Modification date	20141207
dbXrefs	MIM : 609059
	HGNC : HGNC
	Ensembl : ENSG00000177666
	HPRD : 11443
	Vega : OTTHUMG00000133309
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PNPLA2
	BioGPS: 57104
	Gene Expression Atlas: ENSG00000177666
	The Human Protein Atlas: ENSG00000177666
Pathway	NCI Pathway Interaction Database: PNPLA2
	KEGG: PNPLA2
	REACTOME: PNPLA2
	ConsensusPathDB
	Pathway Commons: PNPLA2
Metabolism	MetaCyc: PNPLA2
	HUMANCyc: PNPLA2
Regulation	Ensembl's Regulation: ENSG00000177666
	miRBase: chr11 :818,900-825,571
	TargetScan: NM_020376
	cisRED: ENSG00000177666
Context	iHOP: PNPLA2
	cancer metabolism search in PubMed: PNPLA2
	UCL Cancer Institute: PNPLA2
Assigned class in ccmGDB	C

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Phenotypic Information for PNPLA2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PNPLA2
	Familial Cancer Database: PNPLA2

* 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
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PNPLA2
	MedGen: PNPLA2 (Human Medical Genetics with Condition)
	ClinVar: PNPLA2
Phenotype	MGI: PNPLA2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PNPLA2

Mutations for PNPLA2

* 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 PNPLA2 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
BG960633	PNPLA2	14	243	11	820586	820922	PNPLA2	226	348	11	820923	821042
AV703000	UNC119	1	350	17	26874715	26875703	PNPLA2	345	435	11	825127	825217
BQ446930	PNPLA2	19	113	11	825124	825218	CCDC162P	100	328	6	109669115	109669342
BI017246	PNPLA2	12	262	11	821832	822552	GHITM	255	361	10	85912193	85912300
BU960554	HM13	3	230	20	30154044	30157173	PNPLA2	218	407	11	825028	825217

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=19)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr11:821806-821806	p.S122S	3
chr11:823809-823809	p.P291P	3
chr11:824789-824789	p.L481P	2
chr11:822398-822398	p.R163H	2
chr11:822445-822445	p.K179E	1
chr11:823582-823582	p.R251Q	1
chr11:824428-824428	p.L389L	1
chr11:822460-822460	p.V184M	1
chr11:823725-823725	p.A263A	1
chr11:821962-821962	p.N142S	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	1							1	2		1		1	3		8
# mutation				2	1							1	2		1		1	3		8
nonsynonymous SNV				2	1							1					1	3		5
synonymous SNV													2		1					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
chr11:822398	p.R163H	2
chr11:823736	p.P195L	1
chr11:821962	p.S199S	1
chr11:823779	p.R247H	1
chr11:821973	p.R257R	1
chr11:824015	p.A267V	1
chr11:821985	p.S281S	1
chr11:824410	p.A65V	1
chr11:822402	p.V313M	1
chr11:822471	p.E71Q	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 PNPLA2 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 PNPLA2

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,TMEM259,CD151,CIRBP,D2HGDH,CRACR2B,FAM160A2, JMJD7-PLA2G4B,KANK3,PIDD1,MZF1,NOXA1,PCSK4,PLEKHH3, PNPLA2,RAPGEF3,RASSF7,RNH1,SPSB3,TENC1,ZNF219	ABHD15,ACAA2,ACACB,AGPAT2,ALDH2,AQP7,ADIRF, FAM213A,CAMK1,CEBPA,CIDEC,CSPG4,FAH,HEPN1, LIPE,MLXIPL,PLA2G16,PNPLA2,RDH5,TMEM132C,TYRO3

ABTB1,AQP7,ARRDC2,B3GALT4,BET1L,C14orf180,CD151, CIDEC,GSN,INSR,MADD,MEGF6,MGLL,MOB2, PLCD1,PNPLA2,POLD4,SPSB3,TRADD,YPEL3,ZER1	AGPAT3,ATG9A,C1orf106,CTSD,EPN1,EPS8L2,ESPN, FTH1,FTH1P3,HECTD3,KIAA2013,LOC151534,PIGS,PNPLA2, SLC9A3R1,SPINT1,STARD3,TICAM1,TMEM175,TNIP1,TOM1

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 PNPLA2

There's no related Drug.

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Cross referenced IDs for PNPLA2

* 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