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 PLCB4

Basic gene info.	Gene symbol	PLCB4
	Gene name	phospholipase C, beta 4
	Synonyms	ARCND2\|PI-PLC
	Cytomap	UCSC genome browser: 20p12
	Genomic location	chr20 :9198036-9461462
	Type of gene	protein-coding
	RefGenes	NM_000933.3, NM_001172646.1,NM_182797.2,
	Ensembl id	ENSG00000101333
	Description	1-phosphatidyl-D-myo-inositol-4,5-bisphosphate1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-4PLC-beta-4dJ1119D9.2 (Phopholipase C, beta 4 (1-Phosphatidylinositol-4,5-Bisphosphate Phosphodiesterase Beta 4))inositoltrisphosphohydrolase
	Modification date	20141207
dbXrefs	MIM : 600810
	HGNC : HGNC
	Ensembl : ENSG00000101333
	HPRD : 02885
	Vega : OTTHUMG00000031853
Protein	UniProt: Q15147 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCB4
	BioGPS: 5332
	Gene Expression Atlas: ENSG00000101333
	The Human Protein Atlas: ENSG00000101333
Pathway	NCI Pathway Interaction Database: PLCB4
	KEGG: PLCB4
	REACTOME: PLCB4
	ConsensusPathDB
	Pathway Commons: PLCB4
Metabolism	MetaCyc: PLCB4
	HUMANCyc: PLCB4
Regulation	Ensembl's Regulation: ENSG00000101333
	miRBase: chr20 :9,198,036-9,461,462
	TargetScan: NM_000933
	cisRED: ENSG00000101333
Context	iHOP: PLCB4
	cancer metabolism search in PubMed: PLCB4
	UCL Cancer Institute: PLCB4
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PLCB4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCB4
	Familial Cancer Database: PLCB4

* 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	600810; gene. 600810; gene. 614669; phenotype. 614669; phenotype.
Orphanet	137888; Auriculocondylar syndrome. 137888; Auriculocondylar syndrome.
Disease	KEGG Disease: PLCB4
	MedGen: PLCB4 (Human Medical Genetics with Condition)
	ClinVar: PLCB4
Phenotype	MGI: PLCB4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCB4

Mutations for PLCB4

* 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
ovary	PLCB4	chr20	9309989	9310009		chr20	20828440	20828460

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 PLCB4 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
BE926711	PLCB4	8	389	20	9404462	9417800	PLCB4	387	480	20	9388562	9388655
DA775941	ZC3H7A	1	115	16	11854972	11855086	PLCB4	106	567	20	9351444	9351904
BF346361	PLCB4	582	621	20	9149571	9149611	GBE1	621	648	3	81780156	81780186
AW519364	RNF187	4	97	1	228682575	228682668	PLCB4	88	211	20	9223560	9223685

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=139)	Stat. for Synonymous SNVs (# total SNVs=34)

Stat. for Deletions (# total SNVs=5)	Stat. for Insertions (# total SNVs=2)

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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
chr20:9417698-9417698	p.G876E	5
chr20:9391729-9391729	p.S670L	5
chr20:9404516-9404516	p.R802Q	5
chr20:9449315-9449315	p.E1104K	5
chr20:9364983-9364983	p.T330I	3
chr20:9459645-9459645	p.N1192H	3
chr20:9400450-9400450	p.?	3
chr20:9434098-9434098	p.M983I	3
chr20:9402041-9402041	p.R739Q	3
chr20:9424845-9424845	p.K933N	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=4

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	7		19	2		10		6			24	10	5		2	62	11		11
# mutation	2	7		19	2		10		6			28	10	5		2	74	13		18
nonsynonymous SNV	2	6		18	1		8		5			18	6	3		2	57	11		15
synonymous SNV		1		1	1		2		1			10	4	2			17	2		3

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
chr20:9404516	p.G876E,PLCB4	4
chr20:9417698	p.R802Q,PLCB4	4
chr20:9391729	p.R739L,PLCB4	3
chr20:9449315	p.S670L,PLCB4	3
chr20:9434098	p.M983I,PLCB4	3
chr20:9402041	p.E1104K,PLCB4	3
chr20:9424652	p.K908K,PLCB4	2
chr20:9459613	p.K839N,PLCB4	2
chr20:9438076	p.F39F,PLCB4	2
chr20:9449219	p.R918K,PLCB4	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 PLCB4 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 PLCB4

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


ANKRD36BP1,BTBD3,E2F3,EML4,ESYT3,HNRNPLL,LMO4, LRRC16A,MCM8,MSH6,PADI2,PLCB4,PLCH1,PSME4, RAP2A,SERTAD4,SKP2,TAF4B,TET3,ZNF124,ZNF462	APAF1,BACH1,C11orf30,FAM208A,CASP8AP2,CEP135,JMJD1C, GLTSCR1L,CEP162,KIAA2026,LRCH1,KMT2E,MRE11A,NPAT, PDS5B,PLCB4,RLF,THOC2,TOPBP1,UHRF2,ZNF354B

ASB12,C20orf196,CDS2,CRLS1,CSRP2BP,FERMT1,GPCPD1, NAALADL2,NR1I2,NUDT4,PLCB4,PTPRA,SHROOM4,ST6GAL1, TASP1,TRMT6,TSPAN6,VAV3,ZDHHC9,ZNF343,ZNF41	ADAMTS18,ALOX12B,CCDC129,COL4A6,FKTN,FOXA1,HTR3E, KIAA1804,KREMEN1,LIMD1,FOXD2-AS1,NAPEPLD,PLAGL1,PLCB4, REPS2,SH2D7,SOX9,TAS1R3,TRPM5,ZBTB10,ZNF814

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 PLCB4

There's no related Drug.

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Cross referenced IDs for PLCB4

* 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