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 PLD6

Basic gene info.	Gene symbol	PLD6
	Gene name	phospholipase D family, member 6
	Synonyms	ZUC
	Cytomap	UCSC genome browser: 17p11.2
	Genomic location	chr17 :17104308-17109646
	Type of gene	protein-coding
	RefGenes	NM_178836.3,
	Ensembl id	ENSG00000179598
	Description	PLD 6choline phosphatase 6mitoPLDmitochondrial cardiolipin hydrolasemitochondrial phospholipasephosphatidylcholine-hydrolyzing phospholipase D6phospholipase D6protein zucchini homolog
	Modification date	20141207
dbXrefs	MIM : 614960
	HGNC : HGNC
	Ensembl : ENSG00000179598
	HPRD : 14126
	Vega : OTTHUMG00000059278
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLD6
	BioGPS: 201164
	Gene Expression Atlas: ENSG00000179598
	The Human Protein Atlas: ENSG00000179598
Pathway	NCI Pathway Interaction Database: PLD6
	KEGG: PLD6
	REACTOME: PLD6
	ConsensusPathDB
	Pathway Commons: PLD6
Metabolism	MetaCyc: PLD6
	HUMANCyc: PLD6
Regulation	Ensembl's Regulation: ENSG00000179598
	miRBase: chr17 :17,104,308-17,109,646
	TargetScan: NM_178836
	cisRED: ENSG00000179598
Context	iHOP: PLD6
	cancer metabolism search in PubMed: PLD6
	UCL Cancer Institute: PLD6
Assigned class in ccmGDB	C

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Phenotypic Information for PLD6(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PLD6
	MedGen: PLD6 (Human Medical Genetics with Condition)
	ClinVar: PLD6
Phenotype	MGI: PLD6 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLD6 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
BF732578	PLD6	1	64	17	17109569	17109632	TNS1	58	729	2	218677091	218682697
BC015725	PLD6	1	1829	17	17116084	17124925	IFNAR1	1825	1886	21	34728286	34728347
BI053091	BMP7	34	198	20	55745997	55746161	PLD6	192	406	17	17134619	17134833

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

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

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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=1

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Somatic 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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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
chr17:17106194-17106194	p.F216L	1
chr17:17106230-17106230	p.R204C	1
chr17:17106252-17106252	p.R196R	1
chr17:17106258-17106258	p.Y194Y	1
chr17:17106266-17106266	p.D192N	1
chr17:17106274-17106274	p.T189M	1
chr17:17106395-17106395	p.D149N	1
chr17:17106107-17106107	p.G245S	1
chr17:17109301-17109301	p.A100A	1
chr17:17106133-17106133	p.R236K	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=1

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	3								1		1								2
# mutation	1	3								1		1								2
nonsynonymous SNV	1	2								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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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
chr17:17106266	p.F216L	1
chr17:17106274	p.Y194Y	1
chr17:17106395	p.D192N	1
chr17:17109483	p.T189M	1
chr17:17106133	p.D149N	1
chr17:17106185	p.E40K	1
chr17:17106194	p.R236K	1
chr17:17106258	p.P219S	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 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

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


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

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 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