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 PLCB1

Basic gene info.	Gene symbol	PLCB1
	Gene name	phospholipase C, beta 1 (phosphoinositide-specific)
	Synonyms	EIEE12\|PI-PLC\|PLC-154\|PLC-I\|PLC154\|PLCB1A\|PLCB1B
	Cytomap	UCSC genome browser: 20p12
	Genomic location	chr20 :8113295-8865547
	Type of gene	protein-coding
	RefGenes	NM_015192.3, NM_182734.2,
	Ensembl id	ENSG00000182621
	Description	1-phosphatidyl-D-myo-inositol-4,5-bisphosphate1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1PLC-beta-1inositoltrisphosphohydrolasemonophosphatidylinositol phosphodiesterasephosphoinositidase Cphospholipase C-Itriphosphoinositide p
	Modification date	20141222
dbXrefs	MIM : 607120
	HGNC : HGNC
	Ensembl : ENSG00000182621
	HPRD : 06177
	Vega : OTTHUMG00000031849
Protein	UniProt: Q9NQ66 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCB1
	BioGPS: 23236
	Gene Expression Atlas: ENSG00000182621
	The Human Protein Atlas: ENSG00000182621
Pathway	NCI Pathway Interaction Database: PLCB1
	KEGG: PLCB1
	REACTOME: PLCB1
	ConsensusPathDB
	Pathway Commons: PLCB1
Metabolism	MetaCyc: PLCB1
	HUMANCyc: PLCB1
Regulation	Ensembl's Regulation: ENSG00000182621
	miRBase: chr20 :8,113,295-8,865,547
	TargetScan: NM_015192
	cisRED: ENSG00000182621
Context	iHOP: PLCB1
	cancer metabolism search in PubMed: PLCB1
	UCL Cancer Institute: PLCB1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PLCB1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCB1
	Familial Cancer Database: PLCB1

* 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	607120; gene. 607120; gene. 613722; phenotype. 613722; phenotype.
Orphanet	293181; Malignant migrating partial seizures of infancy. 293181; Malignant migrating partial seizures of infancy. 3451; West syndrome. 3451; West syndrome.
Disease	KEGG Disease: PLCB1
	MedGen: PLCB1 (Human Medical Genetics with Condition)
	ClinVar: PLCB1
Phenotype	MGI: PLCB1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCB1

Mutations for PLCB1

* 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

* 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
breast	PLCB1	chr20	8296860	8296860	PLCB1	chr20	8357007	8357007
large_intestine	PLCB1	chr20	8810913	8810913		chr20	8882215	8882215
ovary	PLCB1	chr20	8608069	8608089	PLCB1	chr20	8646243	8646263
ovary	PLCB1	chr20	8625349	8625369	PLCB1	chr20	8614037	8614057
ovary	PLCB1	chr20	8630133	8630333	CDKAL1	chr6	20668965	20669165
ovary	PLCB1	chr20	8757588	8757608	PLCB1	chr20	8735524	8735544
pancreas	PLCB1	chr20	8357110	8357130		chr20	56389979	56389999
pancreas	PLCB1	chr20	8469553	8469573	PLCB1	chr20	8534994	8535014
pancreas	PLCB1	chr20	8636339	8636359	PLCB1	chr20	8774028	8774048
pancreas	PLCB1	chr20	8726325	8726345	ZNF335	chr20	44589603	44589623
pancreas	PLCB1	chr20	8726326	8726346	ZNF335	chr20	44589603	44589623

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 PLCB1 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
AA984410	PLCB1	1	232	20	8630065	8639283	NLGN2	232	251	17	7320966	7320985
BE835662	PLCB1	4	266	20	8188789	8189060	GTF2A1	265	366	14	81686939	81687040
BF954088	ZSWIM4	149	176	19	13929041	13929072	PLCB1	176	195	20	8226543	8226562
CV383659	PLCB1	7	69	20	8629223	8629285	PLCB1	64	317	20	8618801	8619050

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	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	9	2		2			8		10		5				5	1	3
GAIN (# sample)	8	2		1			6		10		5				5	1	3
LOSS (# sample)	1			1			2

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=155)	Stat. for Synonymous SNVs (# total SNVs=58)

Stat. for Deletions (# total SNVs=3)	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
chr20:8862337-8862337	p.F1164L	5
chr20:8628584-8628584	p.R168C	4
chr20:8755294-8755294	p.Q1013H	4
chr20:8862495-8862495	p.1217	4
chr20:8719917-8719917	p.P740S	4
chr20:8755243-8755243	p.A996A	3
chr20:8769133-8769133	p.Q1050R	3
chr20:8665694-8665694	p.F326L	3
chr20:8665706-8665706	p.S330S	3
chr20:8689378-8689378	p.S410L	3

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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=5

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	5	4		30	1		14	1	2	2		39	13	6	1	1	43	18		15
# mutation	5	4		28	1		14	1	2	2		42	14	6	1	1	62	21		14
nonsynonymous SNV	4	3		18			12	1		2		34	9	6			43	13		7
synonymous SNV	1	1		10	1		2		2			8	5		1	1	19	8		8

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
chr20:8862337	p.F1164F	5
chr20:8689378	p.Q1050R,PLCB1	3
chr20:8769133	p.S410L,PLCB1	3
chr20:8630054	p.R168C,PLCB1	2
chr20:8862318	p.P1158H	2
chr20:8665694	p.Q253Q,PLCB1	2
chr20:8639248	p.S454R,PLCB1	2
chr20:8665706	p.R182W,PLCB1	2
chr20:8698344	p.H866N,PLCB1	2
chr20:8678311	p.G367E,PLCB1	2

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 PLCB1 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 PLCB1

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


ANKRD50,ATRN,BMPR2,BTBD3,SLX4IP,C2orf50,CSNK2A3, EPS8,FRRS1,HOMER1,HUNK,TTI1,NR3C2,OCLN, PLCB1,POU6F2,RALGAPB,RNF24,RPRD1B,TMX4,TOP1	BCLAF1,EPM2AIP1,ESCO1,GOSR1,KDM6A,KRR1,MAP3K7, NAA25,PLCB1,PRPF40A,PUM1,SCAF8,RBM27,RPS6KA5, SMARCAD1,SMC5,SP4,THOC2,USP37,WAPAL,ZNF644

ANKEF1,TMEM230,SLX4IP,CDS2,CSNK2A1,ESF1,FGF13, KIF16B,MAVS,PANK2,PLCB1,PSMF1,PTPRA,RIN2, TASP1,TBC1D20,TMX4,TRMT6,UBOX5,VPS16,ZCCHC3	C16orf45,FAXC,CLIP4,DIXDC1,DPYSL3,DZIP1,EHBP1, EPM2A,GPM6A,NECAB1,NEGR1,PLCB1,RAB11FIP2,RBPMS2, RHOJ,SCD5,SDPR,SMARCA1,SPARCL1,STON1,ZAK

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 PLCB1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	Q9NQ66; -.
Chemistry	ChEMBL	CHEMBL4034; -.
Chemistry	BindingDB	Q9NQ66; -.
Chemistry	ChEMBL	CHEMBL4034; -.
Organism-specific databases	PharmGKB	PA33384; -.
Organism-specific databases	PharmGKB	PA33384; -.
Organism-specific databases	CTD	23236; -.
Organism-specific databases	CTD	23236; -.

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
DB00945	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Acetylsalicylic acid
DB00125	phospholipase C, beta 1 (phosphoinositide-specific)	approved; nutraceutical	L-Arginine
DB00435	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Nitric Oxide
DB00171	phospholipase C, beta 1 (phosphoinositide-specific)	approved; nutraceutical	Adenosine triphosphate
DB00988	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Dopamine
DB00917	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Dinoprostone
DB01240	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Epoprostenol
DB01115	phospholipase C, beta 1 (phosphoinositide-specific)	approved	Nifedipine

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Cross referenced IDs for PLCB1

* 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