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 PLCB2

Basic gene info.	Gene symbol	PLCB2
	Gene name	phospholipase C, beta 2
	Synonyms	PLC-beta-2
	Cytomap	UCSC genome browser: 15q15
	Genomic location	chr15 :40580097-40600174
	Type of gene	protein-coding
	RefGenes	NM_001284297.1, NM_001284298.1,NM_001284299.1,NM_004573.2,
	Ensembl id	ENSG00000137841
	Description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2phosphoinositide phospholipase C-beta-2
	Modification date	20141207
dbXrefs	MIM : 604114
	HGNC : HGNC
	Ensembl : ENSG00000137841
	HPRD : 04985
	Vega : OTTHUMG00000172412
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCB2
	BioGPS: 5330
	Gene Expression Atlas: ENSG00000137841
	The Human Protein Atlas: ENSG00000137841
Pathway	NCI Pathway Interaction Database: PLCB2
	KEGG: PLCB2
	REACTOME: PLCB2
	ConsensusPathDB
	Pathway Commons: PLCB2
Metabolism	MetaCyc: PLCB2
	HUMANCyc: PLCB2
Regulation	Ensembl's Regulation: ENSG00000137841
	miRBase: chr15 :40,580,097-40,600,174
	TargetScan: NM_001284297
	cisRED: ENSG00000137841
Context	iHOP: PLCB2
	cancer metabolism search in PubMed: PLCB2
	UCL Cancer Institute: PLCB2
Assigned class in ccmGDB	C

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Phenotypic Information for PLCB2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCB2
	Familial Cancer Database: PLCB2

* 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 REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: PLCB2
	MedGen: PLCB2 (Human Medical Genetics with Condition)
	ClinVar: PLCB2
Phenotype	MGI: PLCB2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCB2

Mutations for PLCB2

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	PLCB2	chr15	40600138	40600158		chr15	40600738	40600758

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 PLCB2 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
BF893068	PLCB2	3	347	15	40584336	40585879	JUP	342	404	17	39919423	39919485
DA468797	LTBP2	1	337	14	75038461	75038796	PLCB2	333	550	15	40583313	40583530
AK095454	LTBP2	1	337	14	75038461	75038796	PLCB2	333	1974	15	40580109	40583530
BF874520	PLCB2	35	207	15	40585851	40586565	PLCB2	201	530	15	40586570	40588564
N69137	INS-IGF2	4	199	11	2150350	2150546	PLCB2	186	431	15	40593197	40593448
N69126	INS-IGF2	4	199	11	2150350	2150546	PLCB2	186	425	15	40593197	40593439

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=85)	Stat. for Synonymous SNVs (# total SNVs=30)

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
chr15:40582855-40582855	p.K1044N	4
chr15:40583560-40583560	p.R926R	3
chr15:40589767-40589767	p.T426T	3
chr15:40590504-40590504	p.D359Y	2
chr15:40589048-40589048	p.N462T	2
chr15:40594715-40594715	p.D109D	2
chr15:40582856-40582856	p.K1044R	2
chr15:40591421-40591421	p.A197A	2
chr15:40582857-40582857	p.K1044Q	2
chr15:40591423-40591423	p.A197T	2

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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	3	2	1	16	4		5		1	1		12	5	4			13	7	1	11
# mutation	3	2	1	15	4		5		1	1		12	5	4			15	8	1	14
nonsynonymous SNV	1	2	1	7	3		3		1	1		9	5	4			6	6	1	8
synonymous SNV	2			8	1		2					3					9	2		6

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
chr15:40591081	p.S256S,PLCB2	2
chr15:40582855	p.A197A,PLCB2	2
chr15:40582856	p.K1029N,PLCB2	2
chr15:40582857	p.K1029R,PLCB2	2
chr15:40591421	p.K1029E,PLCB2	2
chr15:40586571	p.T630M,PLCB2	1
chr15:40591035	p.P400L,PLCB2	1
chr15:40580971	p.A127A,PLCB2	1
chr15:40589724	p.P1151S,PLCB2	1
chr15:40594168	p.Q1010E,PLCB2	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 PLCB2 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 PLCB2

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


ARHGAP30,ARHGAP9,CARD11,CYTH4,DOK3,FAM78A,FERMT3, FGD2,FMNL1,GAB3,HCLS1,IL10RA,MYO1F,NCF4, PARVG,PIK3R5,PLCB2,RASAL3,SASH3,TNFRSF1B,WAS	ARHGAP30,ARHGAP9,SCIMP,CD53,DOK3,FERMT3,FGD2, GPSM3,IL18,IRF5,ITGAX,KCNAB2,LILRB1,LPXN, MYO1F,PARVG,PLCB2,SASH3,SYK,VAV1,WAS

APBB1IP,ARHGAP25,ARHGAP30,ARHGAP9,BTK,C9orf139,CYTH4, DOCK2,FGD2,HCLS1,IL10RA,IL21R,ITGAL,MYO1G, NCKAP1L,PARVG,PIK3R5,PLCB2,RASAL3,SASH3,WAS	ADAM8,AKNA,BIN2,CARD9,CD4,CYTH4,DEF6, DOCK2,FAM78A,FERMT3,FGD3,IL10RA,MYO1F,MYO1G, NAIP,NDST2,PARVG,PIK3R6,PLCB2,PREX1,VAV1

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 PLCB2

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB01394	phospholipase C, beta 2	approved	Colchicine
DB00988	phospholipase C, beta 2	approved	Dopamine
DB00864	phospholipase C, beta 2	approved; investigational	Tacrolimus
DB00125	phospholipase C, beta 2	approved; nutraceutical	L-Arginine
DB00435	phospholipase C, beta 2	approved	Nitric Oxide

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Cross referenced IDs for PLCB2

* 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