Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPPAP2B
Gene namephosphatidic acid phosphatase type 2B
SynonymsDri42|LPP3|PAP2B|VCIP
CytomapUCSC genome browser: 1p32.2
Genomic locationchr1 :56960418-57045257
Type of geneprotein-coding
RefGenesNM_003713.4,
NM_177414.1,
Ensembl idENSG00000162407
DescriptionPAP2 betalipid phosphate phosphohydrolase 3phosphatidate phosphohydrolase type 2btype-2 phosphatidic acid phosphatase-betavascular endothelial growth factor and type I collagen inducible
Modification date20141207
dbXrefs MIM : 607125
HGNC : HGNC
Ensembl : ENSG00000162407
HPRD : 06179
Vega : OTTHUMG00000008160
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPAP2B
BioGPS: 8613
Gene Expression Atlas: ENSG00000162407
The Human Protein Atlas: ENSG00000162407
PathwayNCI Pathway Interaction Database: PPAP2B
KEGG: PPAP2B
REACTOME: PPAP2B
ConsensusPathDB
Pathway Commons: PPAP2B
MetabolismMetaCyc: PPAP2B
HUMANCyc: PPAP2B
RegulationEnsembl's Regulation: ENSG00000162407
miRBase: chr1 :56,960,418-57,045,257
TargetScan: NM_003713
cisRED: ENSG00000162407
ContextiHOP: PPAP2B
cancer metabolism search in PubMed: PPAP2B
UCL Cancer Institute: PPAP2B
Assigned class in ccmGDBC

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Phenotypic Information for PPAP2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PPAP2B
MedGen: PPAP2B (Human Medical Genetics with Condition)
ClinVar: PPAP2B
PhenotypeMGI: PPAP2B (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPPAP2Bchr15700419657004216chr113343878533438805
ovaryPPAP2Bchr15701512957015149DTX1chr12113505772113505792
pancreasPPAP2Bchr15696356856963588PPAP2Bchr15701103857011058
pancreasPPAP2Bchr15699633656996356PPAP2Bchr15699602356996043
pancreasPPAP2Bchr15702884857028848chr3150598333150598333
pancreasPPAP2Bchr15702884857028848chr3150598347150598347
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPAP2B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BP388129PPAP2B126415696045156960714PHPT12644999139745226139745461
BE930858PPAP2B2016615700497757005126CALM3165388194711219147112551
W23530NOP561612026377242637784PPAP2B4735915696199956962311
BF508320PPAP2B330615696208956977692PPAP2B29940715696110056961208
AK001092WDR261872951224590943224591051PPAP2B294194115703110857036506
BF842389PPAP2B2128815700486657005134PPAP2B28139715700474457004860
AU120214PPAP2B129615703448857034783PPAP2B29475415703604857036506
CV427513PPAP2B6319115700194557002073FOXP118237237131423671314426
BP240903CANX14535179149870179153735PPAP2B45157315704520357045325

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample3       1   1 1  
GAIN (# sample)2       1        
LOSS (# sample)1           1 1  
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr1:56977725-56977725p.R245C3
chr1:57002627-57002627p.A99A3
chr1:56990171-56990171p.I118N2
chr1:56962279-56962279p.E294K2
chr1:56977735-56977735p.T241T2
chr1:56962285-56962285p.R292W2
chr1:56990067-56990067p.R153C2
chr1:56977796-56977796p.R221Q1
chr1:56990070-56990070p.G152W1
chr1:57002645-57002645p.I93I1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample1 23    1  24   8  4
# mutation2 23    1  25   9  4
nonsynonymous SNV1 22    1  23   7  3
synonymous SNV1  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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr1:56990070p.G152W2
chr1:56977725p.E294K2
chr1:56962279p.R292W2
chr1:56962285p.R245C2
chr1:56990067p.V130V1
chr1:57044640p.R107R1
chr1:56977713p.A288V1
chr1:56990134p.L98L1
chr1:56989495p.F272L1
chr1:56990203p.I95I1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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