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 PLD2
Basic gene info.Gene symbolPLD2
Gene namephospholipase D2
Synonyms-
CytomapUCSC genome browser: 17p13.1
Genomic locationchr17 :4710395-4726727
Type of geneprotein-coding
RefGenesNM_001243108.1,
NM_002663.4,
Ensembl idENSG00000129219
DescriptionPLD1Ccholine phosphatase 2hPLD2phosphatidylcholine-hydrolyzing phospholipase D2
Modification date20141222
dbXrefs MIM : 602384
HGNC : HGNC
Ensembl : ENSG00000129219
HPRD : 03857
Vega : OTTHUMG00000090779
ProteinUniProt: O14939
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLD2
BioGPS: 5338
Gene Expression Atlas: ENSG00000129219
The Human Protein Atlas: ENSG00000129219
PathwayNCI Pathway Interaction Database: PLD2
KEGG: PLD2
REACTOME: PLD2
ConsensusPathDB
Pathway Commons: PLD2
MetabolismMetaCyc: PLD2
HUMANCyc: PLD2
RegulationEnsembl's Regulation: ENSG00000129219
miRBase: chr17 :4,710,395-4,726,727
TargetScan: NM_001243108
cisRED: ENSG00000129219
ContextiHOP: PLD2
cancer metabolism search in PubMed: PLD2
UCL Cancer Institute: PLD2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLD2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLD2
Familial Cancer Database: PLD2
* 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_GLYCEROPHOSPHOLIPID_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 602384; gene.
Orphanet
DiseaseKEGG Disease: PLD2
MedGen: PLD2 (Human Medical Genetics with Condition)
ClinVar: PLD2
PhenotypeMGI: PLD2 (International Mouse Phenotyping Consortium)
PhenomicDB: PLD2

Mutations for PLD2
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLD2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG994088CKM8281194581502445818839PLD22743701747145174714613
AI909908PLD24551747213834721440SYTL14514112767595727676205

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 # sample             1   
GAIN (# sample)             1   
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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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=27)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=0)
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
chr17:4721376-4721376p.E632G4
chr17:4721881-4721881p.A701V3
chr17:4719139-4719139p.G457fs*163
chr17:4722778-4722778p.A788V3
chr17:4722785-4722785p.L790L2
chr17:4711611-4711611p.D95N2
chr17:4718838-4718838p.G414D2
chr17:4718853-4718853p.A419V2
chr17:4722448-4722448p.P748L2
chr17:4714224-4714224p.R330W2

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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
# sample13262 1 2  6321 2010111
# mutation13272 1 3  6421 2213111
nonsynonymous SNV 2 5  1 3  52 1 61316
synonymous SNV11222      122  16  5
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
chr17:4721881p.R322R,PLD22
chr17:4711611p.D95N,PLD22
chr17:4714202p.A701V,PLD22
chr17:4713072p.S585Y,PLD21
chr17:4721629p.R720H,PLD21
chr17:4714224p.H894H,PLD21
chr17:4722387p.A136V,PLD21
chr17:4725982p.L592L,PLD21
chr17:4711685p.A728P,PLD21
chr17:4720288p.F178L,PLD21

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 PLD2 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 PLD2

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

ACADVL,CNTROB,CXCL16,CTDNEP1,GEMIN4,INPP5K,CLUH,
KIF1C,MED11,MINK1,MNT,MYBBP1A,NDEL1,NEURL4,
PLD2,PLSCR3,SGSM2,SMG6,TAX1BP3,TMEM102,ZMYND15
ARHGEF19,ASB6,BAIAP2L1,CCDC120,CCDC85C,CLSTN1,ELMO3,
EPS8L2,ITGB4,LIG1,LIMK2,MICALL1,PLD2,PPAP2C,
PPP1R13L,PVRL4,RHBDF1,RTKN,SH2D3A,SSH3,TMPRSS13

ANKFY1,C17orf59,CAMTA2,CNTROB,CXCL16,CTDNEP1,FLII,
FXR2,GABARAP,INPP5K,MINK1,MYO1C,NDEL1,PAFAH1B1,
PLD2,PLSCR3,RAI1,RAP1GAP2,SGSM2,SMG6,ZBTB4
AP2A2,ARAP1,CLK3,CLSTN1,COG1,EDC4,GRN,
KDM4B,LRRK1,MADD,MKNK2,PLD2,PLEKHG3,PLXNA3,
PNPLA7,RECQL5,TBC1D9B,UBE3B,USP19,ZDHHC7,ZNF646
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 PLD2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB O14939; -.
ChemistryChEMBL CHEMBL2734; -.
ChemistryGuidetoPHARMACOLOGY 1434; -.
Organism-specific databasesPharmGKB PA33397; -.
Organism-specific databasesCTD 5338; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00122phospholipase D2approved; nutraceuticalCholine
DB01394phospholipase D2approvedColchicine
DB00988phospholipase D2approvedDopamine
DB00864phospholipase D2approved; investigationalTacrolimus
DB00125phospholipase D2approved; nutraceuticalL-Arginine
DB00435phospholipase D2approvedNitric Oxide


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Cross referenced IDs for PLD2
* 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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