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 PAFAH2

Basic gene info.	Gene symbol	PAFAH2
	Gene name	platelet-activating factor acetylhydrolase 2, 40kDa
	Synonyms	HSD-PLA2
	Cytomap	UCSC genome browser: 1p36
	Genomic location	chr1 :26286257-26324648
	Type of gene	protein-coding
	RefGenes	NM_000437.3,
	Ensembl id	ENSG00000158006
	Description	SD-PLA2platelet-activating factor acetylhydrolase 2, cytoplasmicserine-dependent phospholipase A2
	Modification date	20141207
dbXrefs	MIM : 602344
	HGNC : HGNC
	Ensembl : ENSG00000158006
	HPRD : 03824
	Vega : OTTHUMG00000007437
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PAFAH2
	BioGPS: 5051
	Gene Expression Atlas: ENSG00000158006
	The Human Protein Atlas: ENSG00000158006
Pathway	NCI Pathway Interaction Database: PAFAH2
	KEGG: PAFAH2
	REACTOME: PAFAH2
	ConsensusPathDB
	Pathway Commons: PAFAH2
Metabolism	MetaCyc: PAFAH2
	HUMANCyc: PAFAH2
Regulation	Ensembl's Regulation: ENSG00000158006
	miRBase: chr1 :26,286,257-26,324,648
	TargetScan: NM_000437
	cisRED: ENSG00000158006
Context	iHOP: PAFAH2
	cancer metabolism search in PubMed: PAFAH2
	UCL Cancer Institute: PAFAH2
Assigned class in ccmGDB	C

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Phenotypic Information for PAFAH2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PAFAH2
	Familial Cancer Database: PAFAH2

* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

Others
OMIM
Orphanet
Disease	KEGG Disease: PAFAH2
	MedGen: PAFAH2 (Human Medical Genetics with Condition)
	ClinVar: PAFAH2
Phenotype	MGI: PAFAH2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PAFAH2

Mutations for PAFAH2

* 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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	PAFAH2	chr1	26304802	26304822		chr11	87519189	87519209

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 PAFAH2 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
AI218124	C20orf62	24	351	20	43090411	43090738	PAFAH2	349	546	1	26299106	26301071
AW449898	ROBO2	206	227	3	76950568	76950589	PAFAH2	225	411	1	26287619	26287805
AK129536	ZEB2	1	351	2	145267236	145267586	PAFAH2	346	1590	1	26286260	26287504

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=23)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=1)
There's no deleted 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
chr1:26315958-26315958	p.L75L	2
chr1:26315993-26315993	p.E64K	2
chr1:26311004-26311004	p.A119A	2
chr1:26314754-26314754	p.L103F	2
chr1:26301136-26301136	p.A255V	1
chr1:26317306-26317306	p.?	1
chr1:26310483-26310483	p.R169H	1
chr1:26288568-26288568	p.K364T	1
chr1:26314809-26314809	p.R85H	1
chr1:26303174-26303174	p.R253W	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			3		2			6	1		2
# mutation	1			8	2		1		2			3		2			6	1		3
nonsynonymous SNV	1			5	1		1		2			3		2			2	1		1
synonymous SNV				3	1												4			2

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
chr1:26311004	p.A119A	2
chr1:26303246	p.I280I	1
chr1:26314785	p.A80V	1
chr1:26299085	p.G234G	1
chr1:26303254	p.L75L	1
chr1:26314809	p.R229H	1
chr1:26299107	p.P50P	1
chr1:26310447	p.R229S	1
chr1:26315944	p.Q41Q	1
chr1:26299185	p.D226G	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 PAFAH2 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 PAFAH2

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


SMIM14,DNAJC16,EIF4G3,FBXL5,HMGCL,KIAA0232,KIAA0319L, LRBA,LRRFIP1,PAFAH2,PDIK1L,PDPK1,PIGV,RBM47, RSC1A1,SPG11,TBC1D9,TMBIM6,TMEM57,VPS13D,WDR31	AP1M2,ARSD,ASTN2,C9orf152,CAPN13,CORO2A,CYP2J2, DLG3,EPCAM,ETNK2,FAM174B,ILDR1,KIAA0319L,LEO1, PAFAH2,PPM1H,SLC38A1,SLC39A11,STYK1,TMEM63C,ZNF652

ABCD3,ABHD3,ATP8B1,BCAS1,STPG1,C1orf210,C4orf19, CDS1,CPT2,DHDDS,FUCA1,GGT6,GPA33,HMGCL, NR3C2,PAFAH2,RBM47,RPS6KA1,SLC35A3,SULT1B1,TSPAN1	ACADS,ACSF2,AP1M2,KDF1,C1orf210,CBLC,CPT2, EPB41L4B,ESRRA,GPBP1L1,HDHD3,KLC4,LCMT1,MARVELD3, NAT2,PAFAH2,PROSC,SH3BGRL2,SLC35D2,STAP2,TMEM144

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 PAFAH2

There's no related Drug.

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Cross referenced IDs for PAFAH2

* 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