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 PLCD1

Basic gene info.	Gene symbol	PLCD1
	Gene name	phospholipase C, delta 1
	Synonyms	NDNC3\|PLC-III
	Cytomap	UCSC genome browser: 3p22-p21.3
	Genomic location	chr3 :38048986-38066278
	Type of gene	protein-coding
	RefGenes	NM_001130964.1, NM_006225.3,NR_024071.1,
	Ensembl id	ENSG00000187091
	Description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-11-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1PLC-delta-1phosphoinositide phospholipase C-delta-1phospholipase C-III
	Modification date	20141207
dbXrefs	MIM : 602142
	HGNC : HGNC
	Ensembl : ENSG00000187091
	HPRD : 09073
	Vega : OTTHUMG00000130813
Protein	UniProt: P51178 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCD1
	BioGPS: 5333
	Gene Expression Atlas: ENSG00000187091
	The Human Protein Atlas: ENSG00000187091
Pathway	NCI Pathway Interaction Database: PLCD1
	KEGG: PLCD1
	REACTOME: PLCD1
	ConsensusPathDB
	Pathway Commons: PLCD1
Metabolism	MetaCyc: PLCD1
	HUMANCyc: PLCD1
Regulation	Ensembl's Regulation: ENSG00000187091
	miRBase: chr3 :38,048,986-38,066,278
	TargetScan: NM_001130964
	cisRED: ENSG00000187091
Context	iHOP: PLCD1
	cancer metabolism search in PubMed: PLCD1
	UCL Cancer Institute: PLCD1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PLCD1 in cancer cell metabolism	1. Xiang T, Li L, Fan Y, Jiang Y, Ying Y, et al. (2010) PLCD1 is a functional tumor suppressor inducing G2/M arrest and frequently methylated in breast cancer. Cancer biology & therapy 10: 520-527. go to article

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Phenotypic Information for PLCD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCD1
	Familial Cancer Database: PLCD1

* 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
KEGG_INOSITOL_PHOSPHATE_METABOLISM

Others
OMIM	151600; phenotype. 602142; gene.
Orphanet	2387; Leukonychia totalis.
Disease	KEGG Disease: PLCD1
	MedGen: PLCD1 (Human Medical Genetics with Condition)
	ClinVar: PLCD1
Phenotype	MGI: PLCD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCD1

Mutations for PLCD1

* 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 PLCD1 related fusion information.

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

CN404773

INS-IGF2

111

2153887

2153997

PLCD1

185

38053505

38246281

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=44)	Stat. for Synonymous SNVs (# total SNVs=19)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr3:38052853-38052853	p.I214I	4
chr3:38061700-38061700	p.R60W	3
chr3:38058047-38058047	p.W121*	2
chr3:38050789-38050789	p.R527H	2
chr3:38051251-38051251	p.P447A	2
chr3:38051941-38051941	p.P301P	2
chr3:38051164-38051164	p.R476C	1
chr3:38053062-38053062	p.D177D	1
chr3:38051499-38051499	p.L395V	1
chr3:38061760-38061760	p.R40C	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=3

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	1		12	3		2		2	1		5	2				4	5	1	11
# mutation	1	1		12	3		2		2	1		6	2				5	5	1	11
nonsynonymous SNV	1			10	3		2		2	1		5	1				4	4	1	6
synonymous SNV		1		2								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
chr3:38061700	p.R81W,PLCD1	3
chr3:38052853	p.I235I,PLCD1	3
chr3:38050888	p.R61H,PLCD1	2
chr3:38049554	p.K733N,PLCD1	2
chr3:38061759	p.D515G,PLCD1	2
chr3:38051499	p.T82I,PLCD1	1
chr3:38053064	p.G618W,PLCD1	1
chr3:38049632	p.L391L,PLCD1	1
chr3:38065845	p.N617N,PLCD1	1
chr3:38050579	p.H377Y,PLCD1	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 PLCD1 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 PLCD1

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


ACAN,C16orf90,C4orf51,PXDC1,DSG3,EXTL1,FES, FXYD6,KCNG1,KLK8,MFGE8,PGM5P2,PLCD1,PMP2, RNF222,SLC15A1,SPEG,TFEB,TRPV4,VILL,ZBTB32	B3GALT4,CTDSP1,DDAH2,EML3,HYI,INF2,KIFC3, KLHL22,LMF2,LOC729991,LRP3,MMP24,MXD4,NUCB1, PLCD1,SNX17,TMEM129,TSPAN15,UCK1,UROD,WTIP

ABTB1,B3GALT4,BTD,CACFD1,CAPN5,FBXW5,IL17RC, KIAA0513,MGLL,PDCD4,PLCD1,PNPLA2,PNPLA7,PRKCD, SERINC2,TMEM115,TMEM59,VIPR1,VSIG2,YPEL3,ZER1	ABHD3,AHCYL2,AMACR,CA4,CAPN2,CLCN2,ENPP1, GBA,LIPH,LITAF,MGLL,MKRN1,PEX26,PLCD1, PRDX6,SCNN1A,SLC26A3,SLC4A4,SPATS2L,TJP3,TMEM63B

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 PLCD1

There's no related Drug.

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Cross referenced IDs for PLCD1

* 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