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 PLD3

Basic gene info.	Gene symbol	PLD3
	Gene name	phospholipase D family, member 3
	Synonyms	AD19\|HU-K4\|HUK4
	Cytomap	UCSC genome browser: 19q13.2
	Genomic location	chr19 :40854331-40884390
	Type of gene	protein-coding
	RefGenes	NM_001031696.3, NM_001291311.1,NM_012268.3,
	Ensembl id	ENSG00000105223
	Description	choline phosphatase 3hindIII K4L homologphosphatidylcholine-hydrolyzing phospholipase D3phospholipase D3
	Modification date	20141212
dbXrefs	MIM : 615698
	HGNC : HGNC
	Ensembl : ENSG00000105223
	HPRD : 07148
	Vega : OTTHUMG00000152736
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLD3
	BioGPS: 23646
	Gene Expression Atlas: ENSG00000105223
	The Human Protein Atlas: ENSG00000105223
Pathway	NCI Pathway Interaction Database: PLD3
	KEGG: PLD3
	REACTOME: PLD3
	ConsensusPathDB
	Pathway Commons: PLD3
Metabolism	MetaCyc: PLD3
	HUMANCyc: PLD3
Regulation	Ensembl's Regulation: ENSG00000105223
	miRBase: chr19 :40,854,331-40,884,390
	TargetScan: NM_001031696
	cisRED: ENSG00000105223
Context	iHOP: PLD3
	cancer metabolism search in PubMed: PLD3
	UCL Cancer Institute: PLD3
Assigned class in ccmGDB	C

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Phenotypic Information for PLD3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: PLD3
	MedGen: PLD3 (Human Medical Genetics with Condition)
	ClinVar: PLD3
Phenotype	MGI: PLD3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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.

Sample

Symbol_a

Chr_a

Start_a

End_a

Symbol_b

Chr_b

Start_b

End_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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLD3 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
BE699806	PLD3	11	206	19	40880387	40882570	CPNE5	203	344	6	36790178	36790319
BJ997169	PLD3	1	230	19	40871755	40872571	LOC100507412	227	417	?	109584	109774
AL041531	PLD3	16	87	19	40880484	40882543	PLD3	84	562	19	40882531	40884120
CA310232	PLD3	16	193	19	40884213	40884390	PLD3	187	736	19	40871778	40873781
BE295537	PLD3	1	396	19	40884052	40884397	CAPZA1	397	422	1	113207780	113207809
BE938399	GREB1L	32	215	18	18983889	19019598	PLD3	206	312	19	40880478	40882572

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=3

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Somatic 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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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
chr19:40877707-40877707	p.Y216C	2
chr19:40883999-40883999	p.F411F	2
chr19:40882562-40882562	p.R303C	2
chr19:40884020-40884020	p.P418P	2
chr19:40877594-40877594	p.G178G	2
chr19:40883932-40883932	p.A389V	2
chr19:40873684-40873684	p.W56*	1
chr19:40882661-40882661	p.T336A	1
chr19:40877656-40877656	p.W199L	1
chr19:40883977-40883977	p.R404Q	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=2

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	2	4		7	1							5	2	1			5	4		3
# mutation	2	4		7	1							5	2	1			5	4		4
nonsynonymous SNV	2	2		6								4	1					4		4
synonymous SNV		2		1	1							1	1	1			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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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
chr19:40883999	p.G231G,PLD3	2
chr19:40877594	p.F464F,PLD3	2
chr19:40872766	p.R73R,PLD3	1
chr19:40884063	p.R356H,PLD3	1
chr19:40877716	p.E87K,PLD3	1
chr19:40882661	p.R375W,PLD3	1
chr19:40872767	p.A108A,PLD3	1
chr19:40877731	p.A376P,PLD3	1
chr19:40883698	p.N132S,PLD3	1
chr19:40872796	p.R385H,PLD3	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 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

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


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

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 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