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 symbolPLCB2
Gene namephospholipase C, beta 2
SynonymsPLC-beta-2
CytomapUCSC genome browser: 15q15
Genomic locationchr15 :40580097-40600174
Type of geneprotein-coding
RefGenesNM_001284297.1,
NM_001284298.1,NM_001284299.1,NM_004573.2,
Ensembl idENSG00000137841
Description1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-2phosphoinositide phospholipase C-beta-2
Modification date20141207
dbXrefs MIM : 604114
HGNC : HGNC
Ensembl : ENSG00000137841
HPRD : 04985
Vega : OTTHUMG00000172412
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCB2
BioGPS: 5330
Gene Expression Atlas: ENSG00000137841
The Human Protein Atlas: ENSG00000137841
PathwayNCI Pathway Interaction Database: PLCB2
KEGG: PLCB2
REACTOME: PLCB2
ConsensusPathDB
Pathway Commons: PLCB2
MetabolismMetaCyc: PLCB2
HUMANCyc: PLCB2
RegulationEnsembl's Regulation: ENSG00000137841
miRBase: chr15 :40,580,097-40,600,174
TargetScan: NM_001284297
cisRED: ENSG00000137841
ContextiHOP: PLCB2
cancer metabolism search in PubMed: PLCB2
UCL Cancer Institute: PLCB2
Assigned class in ccmGDBC

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Phenotypic Information for PLCB2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PLCB2
MedGen: PLCB2 (Human Medical Genetics with Condition)
ClinVar: PLCB2
PhenotypeMGI: PLCB2 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasPLCB2chr154060013840600158chr154060073840600758
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLCB2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF893068PLCB23347154058433640585879JUP342404173991942339919485
DA468797LTBP21337147503846175038796PLCB2333550154058331340583530
AK095454LTBP21337147503846175038796PLCB23331974154058010940583530
BF874520PLCB235207154058585140586565PLCB2201530154058657040588564
N69137INS-IGF241991121503502150546PLCB2186431154059319740593448
N69126INS-IGF241991121503502150546PLCB2186425154059319740593439

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy 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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr15:40582855-40582855p.K1044N4
chr15:40583560-40583560p.R926R3
chr15:40589767-40589767p.T426T3
chr15:40590504-40590504p.D359Y2
chr15:40589048-40589048p.N462T2
chr15:40594715-40594715p.D109D2
chr15:40582856-40582856p.K1044R2
chr15:40591421-40591421p.A197A2
chr15:40582857-40582857p.K1044Q2
chr15:40591423-40591423p.A197T2

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample321164 5 11 1254  137111
# mutation321154 5 11 1254  158114
nonsynonymous SNV12173 3 11 954  6618
synonymous SNV2  81 2    3    92 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr15:40591081p.S256S,PLCB22
chr15:40582855p.A197A,PLCB22
chr15:40582856p.K1029N,PLCB22
chr15:40582857p.K1029R,PLCB22
chr15:40591421p.K1029E,PLCB22
chr15:40594162p.F656F,PLCB21
chr15:40582813p.L405L,PLCB21
chr15:40589094p.D306V,PLCB21
chr15:40590478p.G163G,PLCB21
chr15:40594805p.D1024N,PLCB21

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01394phospholipase C, beta 2approvedColchicine
DB00988phospholipase C, beta 2approvedDopamine
DB00864phospholipase C, beta 2approved; investigationalTacrolimus
DB00125phospholipase C, beta 2approved; nutraceuticalL-Arginine
DB00435phospholipase C, beta 2approvedNitric 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



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