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 PLD6
Basic gene info.Gene symbolPLD6
Gene namephospholipase D family, member 6
SynonymsZUC
CytomapUCSC genome browser: 17p11.2
Genomic locationchr17 :17104308-17109646
Type of geneprotein-coding
RefGenesNM_178836.3,
Ensembl idENSG00000179598
DescriptionPLD 6choline phosphatase 6mitoPLDmitochondrial cardiolipin hydrolasemitochondrial phospholipasephosphatidylcholine-hydrolyzing phospholipase D6phospholipase D6protein zucchini homolog
Modification date20141207
dbXrefs MIM : 614960
HGNC : HGNC
Ensembl : ENSG00000179598
HPRD : 14126
Vega : OTTHUMG00000059278
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLD6
BioGPS: 201164
Gene Expression Atlas: ENSG00000179598
The Human Protein Atlas: ENSG00000179598
PathwayNCI Pathway Interaction Database: PLD6
KEGG: PLD6
REACTOME: PLD6
ConsensusPathDB
Pathway Commons: PLD6
MetabolismMetaCyc: PLD6
HUMANCyc: PLD6
RegulationEnsembl's Regulation: ENSG00000179598
miRBase: chr17 :17,104,308-17,109,646
TargetScan: NM_178836
cisRED: ENSG00000179598
ContextiHOP: PLD6
cancer metabolism search in PubMed: PLD6
UCL Cancer Institute: PLD6
Assigned class in ccmGDBC

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Phenotypic Information for PLD6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLD6
Familial Cancer Database: PLD6
* 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: PLD6
MedGen: PLD6 (Human Medical Genetics with Condition)
ClinVar: PLD6
PhenotypeMGI: PLD6 (International Mouse Phenotyping Consortium)
PhenomicDB: PLD6

Mutations for PLD6
* 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 PLD6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF732578PLD6164171710956917109632TNS1587292218677091218682697
BC015725PLD611829171711608417124925IFNAR118251886213472828634728347
BI053091BMP734198205574599755746161PLD6192406171713461917134833

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
There's no copy number variation information in COSMIC data for this gene.

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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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr17:17106266-17106266p.D192N1
chr17:17106274-17106274p.T189M1
chr17:17106395-17106395p.D149N1
chr17:17106107-17106107p.G245S1
chr17:17109301-17109301p.A100A1
chr17:17106133-17106133p.R236K1
chr17:17109483-17109483p.E40K1
chr17:17106180-17106180p.K220N1
chr17:17109597-17109597p.G2*1
chr17:17106185-17106185p.P219S1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample13       1 1       2
# mutation13       1 1       2
nonsynonymous SNV12       1 1       2
synonymous SNV 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
chr17:17109483p.R236K1
chr17:17106133p.P219S1
chr17:17106185p.F216L1
chr17:17106194p.Y194Y1
chr17:17106258p.D192N1
chr17:17106266p.T189M1
chr17:17106274p.D149N1
chr17:17106395p.E40K1

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 PLD6 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 PLD6

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

ATPAF2,GID4,CASKIN1,COPS3,DHX29,FLCN,HIGD1C,
IGF2BP1,KLK12,KLK14,KRTAP6-2,KRTAP6-3,LOC200726,MED9,
NPHP3-AS1,NT5M,PEMT,PLD6,PRPSAP2,SKIV2L2,TTC19
ABCD2,ACVR1C,ADIPOQ,FAM219B,CABLES1,CBLN1,CPM,
EHHADH,EIF4EBP2,FAM13A,FZD4,GABRE,LPL,PCK1,
PDP2,PEX11A,PEX19,PHKA2,PKD1L2,PLD6,SLC7A10

ACTR3B,AURKB,FAM216A,DVL2,FAHD2B,GLS2,GTPBP3,
HTRA2,IMP4,LOC284023,LOC729234,LOC92659,MAP6D1,MYBBP1A,
NT5M,PLD6,PVT1,SDCCAG3,SH2D2A,SIGMAR1,WNT8B
CHST10,COPZ2,ENOX1,FIBIN,GNAI2,HAND2,KCNJ8,
KLHDC8B,KLHL21,MEOX2,MITF,PELI3,PGM5P2,PHLDA3,
PLD6,PPAPDC3,PRDM8,RAB34,TBKBP1,TMEM55A,TTC7B
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 PLD6


There's no related Drug.
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Cross referenced IDs for PLD6
* 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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