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 PPAP2A

Basic gene info.	Gene symbol	PPAP2A
	Gene name	phosphatidic acid phosphatase type 2A
	Synonyms	LLP1a\|LPP1\|PAP-2a\|PAP2
	Cytomap	UCSC genome browser: 5q11
	Genomic location	chr5 :54720682-54830873
	Type of gene	protein-coding
	RefGenes	NM_003711.3, NM_176895.2,NR_103485.1,
	Ensembl id	ENSG00000067113
	Description	lipid phosphate phosphohydrolase 1lipid phosphate phosphohydrolase 1aphosphatidate phosphohydrolase type 2aphosphatidic acid phosphatase 2aphosphatidic acid phosphohydrolase type 2atype-2 phosphatidic acid phosphatase alpha
	Modification date	20141207
dbXrefs	MIM : 607124
	HGNC : HGNC
	Ensembl : ENSG00000067113
	HPRD : 06178
	Vega : OTTHUMG00000162240
Protein	UniProt: O14494 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPAP2A
	BioGPS: 8611
	Gene Expression Atlas: ENSG00000067113
	The Human Protein Atlas: ENSG00000067113
Pathway	NCI Pathway Interaction Database: PPAP2A
	KEGG: PPAP2A
	REACTOME: PPAP2A
	ConsensusPathDB
	Pathway Commons: PPAP2A
Metabolism	MetaCyc: PPAP2A
	HUMANCyc: PPAP2A
Regulation	Ensembl's Regulation: ENSG00000067113
	miRBase: chr5 :54,720,682-54,830,873
	TargetScan: NM_003711
	cisRED: ENSG00000067113
Context	iHOP: PPAP2A
	cancer metabolism search in PubMed: PPAP2A
	UCL Cancer Institute: PPAP2A
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PPAP2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPAP2A
	Familial Cancer Database: PPAP2A

* 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_GLYCEROLIPID_METABOLISM KEGG_GLYCEROPHOSPHOLIPID_METABOLISM KEGG_SPHINGOLIPID_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM	607124; gene.
Orphanet
Disease	KEGG Disease: PPAP2A
	MedGen: PPAP2A (Human Medical Genetics with Condition)
	ClinVar: PPAP2A
Phenotype	MGI: PPAP2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPAP2A

Mutations for PPAP2A

* 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
ovary	PPAP2A	chr5	54804178	54804198	MYCBP2	chr13	77788329	77788349
prostate	PPAP2A	chr5	54737392	54737392	PPAP2A	chr5	54748476	54748476
prostate	PPAP2A	chr5	54743574	54743574	PPAP2A	chr5	54774361	54774361

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 PPAP2A 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
AA505717	ARFGEF1	18	327	8	68109197	68109509	PPAP2A	310	449	5	54821389	54821528
BE710077	GGCT	12	387	7	30539689	30540064	PPAP2A	382	449	5	54788745	54788812

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=16)	Stat. for Synonymous SNVs (# total SNVs=7)

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
chr5:54721866-54721866	p.L185P	2
chr5:54721717-54721717	p.Q235*	1
chr5:54763810-54763810	p.L127L	1
chr5:54721739-54721739	p.S227S	1
chr5:54763841-54763841	p.T117S	1
chr5:54721040-54721054	p.P280_Q284delPSNHQ	1
chr5:54721756-54721756	p.Y222D	1
chr5:54763842-54763842	p.T117A	1
chr5:54721043-54721043	p.H283Q	1
chr5:54721768-54721768	p.R218*	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	2	1		6					1		1	1	1	1				1		6
# mutation	3	1		6					1		1	1	1	1				1		6
nonsynonymous SNV	3	1		2							1			1				1		6
synonymous SNV				4					1			1	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
chr5:54721866	p.L184P,PPAP2A	2
chr5:54771192	p.I141I,PPAP2A	1
chr5:54721867	p.G124D,PPAP2A	1
chr5:54771275	p.A101V,PPAP2A	1
chr5:54721117	p.E258Q,PPAP2A	1
chr5:54737683	p.K100T,PPAP2A	1
chr5:54786889	p.T254T,PPAP2A	1
chr5:54721127	p.A96A,PPAP2A	1
chr5:54737704	p.R253K,PPAP2A	1
chr5:54721131	p.N93T,PPAP2A	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 PPAP2A 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 PPAP2A

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


CD34,CDH5,CLEC14A,CNRIP1,CXorf36,EBF1,EMCN, ERG,ESAM,FAM162B,GJA4,GNG11,JAM2,LDB2, LHFP,MMRN2,MYCT1,PLVAP,PPAP2A,S1PR1,THSD1	AKR1C3,ANXA5,ASAH1,CALM1,CAV1,COPZ2,CRTAP, CYB5R3,FADS3,ITGB1BP1,MBD2,MGST1,MMP28,PICALM, PIR,PPAP2A,RHOA,SERPINF1,SOD3,STEAP1,TPST2

ABCC9,AOC3,CCL14,CHRDL1,ACKR1,MICU3,EMCN, FERMT2,JAM2,LDB2,MEIS1,NEGR1,NKAPL,PPAP2A, RASL12,RBMS3,SDPR,SPARCL1,TLL1,TMEM200B,ZEB1	ABHD4,BMP3,GINM1,CEACAM7,ENPP1,GNA13,GPR37L1, IL4R,CIPC,MAP1LC3B,MXI1,NRBP1,PAFAH1B1,PPAP2A, PPP1CB,RELL1,SLC16A1,SLC26A3,SPAG9,TAB2,VAPA

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 PPAP2A

There's no related Drug.

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Cross referenced IDs for PPAP2A

* 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