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 symbolPLCB4
Gene namephospholipase C, beta 4
SynonymsARCND2|PI-PLC
CytomapUCSC genome browser: 20p12
Genomic locationchr20 :9198036-9461462
Type of geneprotein-coding
RefGenesNM_000933.3,
NM_001172646.1,NM_182797.2,
Ensembl idENSG00000101333
Description1-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 date20141207
dbXrefs MIM : 600810
HGNC : HGNC
Ensembl : ENSG00000101333
HPRD : 02885
Vega : OTTHUMG00000031853
ProteinUniProt: Q15147
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCB4
BioGPS: 5332
Gene Expression Atlas: ENSG00000101333
The Human Protein Atlas: ENSG00000101333
PathwayNCI Pathway Interaction Database: PLCB4
KEGG: PLCB4
REACTOME: PLCB4
ConsensusPathDB
Pathway Commons: PLCB4
MetabolismMetaCyc: PLCB4
HUMANCyc: PLCB4
RegulationEnsembl's Regulation: ENSG00000101333
miRBase: chr20 :9,198,036-9,461,462
TargetScan: NM_000933
cisRED: ENSG00000101333
ContextiHOP: PLCB4
cancer metabolism search in PubMed: PLCB4
UCL Cancer Institute: PLCB4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLCB4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM

check002.gifOthers
OMIM 600810; gene.
600810; gene.
614669; phenotype.
614669; phenotype.
Orphanet 137888; Auriculocondylar syndrome.
137888; Auriculocondylar syndrome.
DiseaseKEGG Disease: PLCB4
MedGen: PLCB4 (Human Medical Genetics with Condition)
ClinVar: PLCB4
PhenotypeMGI: PLCB4 (International Mouse Phenotyping Consortium)
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.

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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPLCB4chr2093099899310009chr202082844020828460
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 PLCB4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE926711PLCB483892094044629417800PLCB43874802093885629388655
DA775941ZC3H7A1115161185497211855086PLCB41065672093514449351904
BF346361PLCB45826212091495719149611GBE162164838178015681780186
AW519364RNF1874971228682575228682668PLCB4882112092235609223685

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample4     2 2     1 1
GAIN (# sample)2     2 2     1 1
LOSS (# sample)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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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=6

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check002.gifSomatic 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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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
chr20:9449315-9449315p.E1104K5
chr20:9391729-9391729p.S670L5
chr20:9404516-9404516p.R802Q5
chr20:9417698-9417698p.G876E5
chr20:9434098-9434098p.M983I3
chr20:9364983-9364983p.T330I3
chr20:9400450-9400450p.?3
chr20:9402041-9402041p.R739Q3
chr20:9459645-9459645p.N1192H3
chr20:9417795-9417795p.K908K2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample27 192 10 6  24105 26211 11
# mutation27 192 10 6  28105 27413 18
nonsynonymous SNV26 181 8 5  1863 25711 15
synonymous SNV 1 11 2 1  1042  172 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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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
chr20:9404516p.G876E,PLCB44
chr20:9417698p.R802Q,PLCB44
chr20:9391729p.R739L,PLCB43
chr20:9449315p.E1104K,PLCB43
chr20:9434098p.S670L,PLCB43
chr20:9402041p.M983I,PLCB43
chr20:9449219p.E513K,PLCB42
chr20:9416235p.R1178Q,PLCB42
chr20:9376218p.K839N,PLCB42
chr20:9438112p.K908K,PLCB42

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 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

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

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
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 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



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