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 PLD3
Basic gene info.Gene symbolPLD3
Gene namephospholipase D family, member 3
SynonymsAD19|HU-K4|HUK4
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :40854331-40884390
Type of geneprotein-coding
RefGenesNM_001031696.3,
NM_001291311.1,NM_012268.3,
Ensembl idENSG00000105223
Descriptioncholine phosphatase 3hindIII K4L homologphosphatidylcholine-hydrolyzing phospholipase D3phospholipase D3
Modification date20141212
dbXrefs MIM : 615698
HGNC : HGNC
Ensembl : ENSG00000105223
HPRD : 07148
Vega : OTTHUMG00000152736
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLD3
BioGPS: 23646
Gene Expression Atlas: ENSG00000105223
The Human Protein Atlas: ENSG00000105223
PathwayNCI Pathway Interaction Database: PLD3
KEGG: PLD3
REACTOME: PLD3
ConsensusPathDB
Pathway Commons: PLD3
MetabolismMetaCyc: PLD3
HUMANCyc: PLD3
RegulationEnsembl's Regulation: ENSG00000105223
miRBase: chr19 :40,854,331-40,884,390
TargetScan: NM_001031696
cisRED: ENSG00000105223
ContextiHOP: PLD3
cancer metabolism search in PubMed: PLD3
UCL Cancer Institute: PLD3
Assigned class in ccmGDBC

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Phenotypic Information for PLD3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLD3
Familial Cancer Database: PLD3
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLD3
MedGen: PLD3 (Human Medical Genetics with Condition)
ClinVar: PLD3
PhenotypeMGI: PLD3 (International Mouse Phenotyping Consortium)
PhenomicDB: PLD3

Mutations for PLD3
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PLD3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE699806PLD311206194088038740882570CPNE520334463679017836790319
BJ997169PLD31230194087175540872571LOC100507412227417?109584109774
AL041531PLD31687194088048440882543PLD384562194088253140884120
CA310232PLD316193194088421340884390PLD3187736194087177840873781
BE295537PLD31396194088405240884397CAPZA13974221113207780113207809
BE938399GREB1L32215181898388919019598PLD3206312194088047840882572

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        3 2      
GAIN (# sample)        3 2      
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr19:40877707-40877707p.Y216C2
chr19:40883999-40883999p.F411F2
chr19:40882562-40882562p.R303C2
chr19:40884020-40884020p.P418P2
chr19:40877594-40877594p.G178G2
chr19:40883932-40883932p.A389V2
chr19:40873684-40873684p.W56*1
chr19:40882661-40882661p.T336A1
chr19:40877656-40877656p.W199L1
chr19:40883977-40883977p.R404Q1

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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
# sample24 71      521  54 3
# mutation24 71      521  54 4
nonsynonymous SNV22 6       41    4 4
synonymous SNV 2 11      111  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
chr19:40883999p.G231G,PLD32
chr19:40877594p.F464F,PLD32
chr19:40872766p.R73R,PLD31
chr19:40884063p.R356H,PLD31
chr19:40877716p.E87K,PLD31
chr19:40882661p.R375W,PLD31
chr19:40872767p.A108A,PLD31
chr19:40877731p.A376P,PLD31
chr19:40883698p.N132S,PLD31
chr19:40872796p.R385H,PLD31

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 PLD3 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 PLD3

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

APOE,C1QA,CHST12,CYBA,DOK2,FOLR2,FTL,
GRN,LMF2,MAN2B1,MGAT1,NUCB1,OSCAR,PLD3,
RCN3,SDF4,SHKBP1,SIRT2,SPI1,TWF2,TYROBP
ACP5,ARPC1B,ARRB2,CATSPER1,CD300C,DOK2,FCGRT,
GRN,HCST,HK3,IFI30,ITGB2,LSP1,MAN2B1,
PILRA,PLA2G15,PLD3,SLC15A3,SPI1,TCIRG1,TYROBP

C1QA,C1QB,C1QC,CD14,CD4,CD86,DOK2,
HAVCR2,HCST,ITGB2,LAIR1,LAPTM5,LILRB4,LRRC25,
MS4A4A,PLD3,PLEKHO2,PSAP,SIGLEC7,SPI1,TYROBP
AKR1B1,M1AP,CSF1R,DNASE2,DPP7,EVA1B,GBGT1,
GGTA1P,GPR137B,HOMER3,HSD17B14,MAFB,MXD4,OSCAR,
PCIF1,PLD3,RASGRP4,RENBP,RNF130,TMEM86A,TSPAN4
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 PLD3


There's no related Drug.
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Cross referenced IDs for PLD3
* 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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