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 PPAP2B

Basic gene info.	Gene symbol	PPAP2B
	Gene name	phosphatidic acid phosphatase type 2B
	Synonyms	Dri42\|LPP3\|PAP2B\|VCIP
	Cytomap	UCSC genome browser: 1p32.2
	Genomic location	chr1 :56960418-57045257
	Type of gene	protein-coding
	RefGenes	NM_003713.4, NM_177414.1,
	Ensembl id	ENSG00000162407
	Description	PAP2 betalipid phosphate phosphohydrolase 3phosphatidate phosphohydrolase type 2btype-2 phosphatidic acid phosphatase-betavascular endothelial growth factor and type I collagen inducible
	Modification date	20141207
dbXrefs	MIM : 607125
	HGNC : HGNC
	Ensembl : ENSG00000162407
	HPRD : 06179
	Vega : OTTHUMG00000008160
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPAP2B
	BioGPS: 8613
	Gene Expression Atlas: ENSG00000162407
	The Human Protein Atlas: ENSG00000162407
Pathway	NCI Pathway Interaction Database: PPAP2B
	KEGG: PPAP2B
	REACTOME: PPAP2B
	ConsensusPathDB
	Pathway Commons: PPAP2B
Metabolism	MetaCyc: PPAP2B
	HUMANCyc: PPAP2B
Regulation	Ensembl's Regulation: ENSG00000162407
	miRBase: chr1 :56,960,418-57,045,257
	TargetScan: NM_003713
	cisRED: ENSG00000162407
Context	iHOP: PPAP2B
	cancer metabolism search in PubMed: PPAP2B
	UCL Cancer Institute: PPAP2B
Assigned class in ccmGDB	C

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Phenotypic Information for PPAP2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPAP2B
	Familial Cancer Database: PPAP2B

* 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
Orphanet
Disease	KEGG Disease: PPAP2B
	MedGen: PPAP2B (Human Medical Genetics with Condition)
	ClinVar: PPAP2B
Phenotype	MGI: PPAP2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPAP2B

Mutations for PPAP2B

* 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	PPAP2B	chr1	57004196	57004216		chr11	33438785	33438805
ovary	PPAP2B	chr1	57015129	57015149	DTX1	chr12	113505772	113505792
pancreas	PPAP2B	chr1	56963568	56963588	PPAP2B	chr1	57011038	57011058
pancreas	PPAP2B	chr1	56996336	56996356	PPAP2B	chr1	56996023	56996043
pancreas	PPAP2B	chr1	57028848	57028848		chr3	150598333	150598333
pancreas	PPAP2B	chr1	57028848	57028848		chr3	150598347	150598347

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 PPAP2B 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
BP388129	PPAP2B	1	264	1	56960451	56960714	PHPT1	264	499	9	139745226	139745461
BE930858	PPAP2B	20	166	1	57004977	57005126	CALM3	165	388	19	47112191	47112551
W23530	NOP56	1	61	20	2637724	2637784	PPAP2B	47	359	1	56961999	56962311
BF508320	PPAP2B	3	306	1	56962089	56977692	PPAP2B	299	407	1	56961100	56961208
AK001092	WDR26	187	295	1	224590943	224591051	PPAP2B	294	1941	1	57031108	57036506
BF842389	PPAP2B	21	288	1	57004866	57005134	PPAP2B	281	397	1	57004744	57004860
AU120214	PPAP2B	1	296	1	57034488	57034783	PPAP2B	294	754	1	57036048	57036506
CV427513	PPAP2B	63	191	1	57001945	57002073	FOXP1	182	372	3	71314236	71314426
BP240903	CANX	1	453	5	179149870	179153735	PPAP2B	451	573	1	57045203	57045325

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=22)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr1:56977725-56977725	p.R245C	3
chr1:57002627-57002627	p.A99A	3
chr1:56962279-56962279	p.E294K	2
chr1:56977735-56977735	p.T241T	2
chr1:56962285-56962285	p.R292W	2
chr1:56990067-56990067	p.R153C	2
chr1:56990171-56990171	p.I118N	2
chr1:56977704-56977704	p.H252N	1
chr1:57002717-57002717	p.N69K	1
chr1:56989949-56989949	p.R192M	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		2	3					1			2	4				8			4
# mutation	2		2	3					1			2	5				9			4
nonsynonymous SNV	1		2	2					1			2	3				7			3
synonymous SNV	1			1									2				2			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
chr1:56962279	p.G152W	2
chr1:56962285	p.E294K	2
chr1:56990070	p.R292W	2
chr1:56977725	p.R245C	2
chr1:56989547	p.L159F	1
chr1:57002639	p.R153C	1
chr1:56989949	p.V130V	1
chr1:57002660	p.R107R	1
chr1:56990007	p.A288V	1
chr1:57002716	p.L98L	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 PPAP2B 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 PPAP2B

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


ARHGAP20,FOXO1,GPR116,KCTD12,LDB2,LHFP,MCTP1, PKD2,PLSCR4,PPAP2B,RCBTB2,RHOJ,SLIT2,SPARCL1, SPRY1,STARD8,SVEP1,TGFBR2,TNS1,TSHZ2,ZNF366	ABCA8,AGTR1,ANTXR2,AZI2,VSTM4,CCDC50,CD302, CRYBG3,FBLN5,LOC100190938,LOC283392,NPR2,PID1,PLSCR4, PPAP2B,PVRL3,RECK,RFTN2,RNF144A,SLC19A3,TCF4

A2M,ARHGEF15,CYYR1,EMCN,ERG,FLRT2,ITPR1, JAM2,LDB2,LHFP,MGP,MMRN2,MYCT1,PABPC5, PDE1A,PODN,PPAP2B,PRICKLE1,QKI,RBMS3,RECK	ARID5B,CORO2B,CPZ,ECM1,FAM180A,FBLN1,FBLN2, FBLN5,FLT1,GRID1,HRC,IGSF10,KRT24,LTBP2, MRC2,NPR1,PLVAP,PPAP2B,SCARA5,SH3BP5,SLC17A7

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 PPAP2B

There's no related Drug.

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Cross referenced IDs for PPAP2B

* 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