Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPLCB1
Gene namephospholipase C, beta 1 (phosphoinositide-specific)
SynonymsEIEE12|PI-PLC|PLC-154|PLC-I|PLC154|PLCB1A|PLCB1B
CytomapUCSC genome browser: 20p12
Genomic locationchr20 :8113295-8865547
Type of geneprotein-coding
RefGenesNM_015192.3,
NM_182734.2,
Ensembl idENSG00000182621
Description1-phosphatidyl-D-myo-inositol-4,5-bisphosphate1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase beta-1PLC-beta-1inositoltrisphosphohydrolasemonophosphatidylinositol phosphodiesterasephosphoinositidase Cphospholipase C-Itriphosphoinositide p
Modification date20141222
dbXrefs MIM : 607120
HGNC : HGNC
Ensembl : ENSG00000182621
HPRD : 06177
Vega : OTTHUMG00000031849
ProteinUniProt: Q9NQ66
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCB1
BioGPS: 23236
Gene Expression Atlas: ENSG00000182621
The Human Protein Atlas: ENSG00000182621
PathwayNCI Pathway Interaction Database: PLCB1
KEGG: PLCB1
REACTOME: PLCB1
ConsensusPathDB
Pathway Commons: PLCB1
MetabolismMetaCyc: PLCB1
HUMANCyc: PLCB1
RegulationEnsembl's Regulation: ENSG00000182621
miRBase: chr20 :8,113,295-8,865,547
TargetScan: NM_015192
cisRED: ENSG00000182621
ContextiHOP: PLCB1
cancer metabolism search in PubMed: PLCB1
UCL Cancer Institute: PLCB1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLCB1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
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.
DiseaseKEGG Disease: PLCB1
MedGen: PLCB1 (Human Medical Genetics with Condition)
ClinVar: PLCB1
PhenotypeMGI: PLCB1 (International Mouse Phenotyping Consortium)
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.

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
breastPLCB1chr2082968608296860PLCB1chr2083570078357007
large_intestinePLCB1chr2088109138810913chr2088822158882215
ovaryPLCB1chr2086080698608089PLCB1chr2086462438646263
ovaryPLCB1chr2086253498625369PLCB1chr2086140378614057
ovaryPLCB1chr2086301338630333CDKAL1chr62066896520669165
ovaryPLCB1chr2087575888757608PLCB1chr2087355248735544
pancreasPLCB1chr2083571108357130chr205638997956389999
pancreasPLCB1chr2084695538469573PLCB1chr2085349948535014
pancreasPLCB1chr2086363398636359PLCB1chr2087740288774048
pancreasPLCB1chr2087263258726345ZNF335chr204458960344589623
pancreasPLCB1chr2087263268726346ZNF335chr204458960344589623
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 PLCB1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA984410PLCB112322086300658639283NLGN22322511773209667320985
BE835662PLCB142662081887898189060GTF2A1265366148168693981687040
BF954088ZSWIM4149176191392904113929072PLCB11761952082265438226562
CV383659PLCB17692086292238629285PLCB1643172086188018619050

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 # sample92 2  8 10 5   513
GAIN (# sample)82 1  6 10 5   513
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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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=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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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
chr20:8862337-8862337p.F1164L5
chr20:8755294-8755294p.Q1013H4
chr20:8628584-8628584p.R168C4
chr20:8862495-8862495p.*1217*4
chr20:8719917-8719917p.P740S4
chr20:8665694-8665694p.F326L3
chr20:8665706-8665706p.S330S3
chr20:8689378-8689378p.S410L3
chr20:8608995-8608995p.R101C3
chr20:8707987-8707987p.F570L3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample54 301 14122 39136114318 15
# mutation54 281 14122 42146116221 14
nonsynonymous SNV43 18  121 2 3496  4313 7
synonymous SNV11 101 2 2  85 11198 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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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
chr20:8862337p.F1164F5
chr20:8689378p.Q1050R,PLCB13
chr20:8769133p.S410L,PLCB13
chr20:8630054p.S454R,PLCB12
chr20:8862318p.R182W,PLCB12
chr20:8665694p.H866N,PLCB12
chr20:8639248p.G367E,PLCB12
chr20:8665706p.R184R,PLCB12
chr20:8698344p.R101H,PLCB12
chr20:8678311p.G476E,PLCB12

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 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

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

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
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 PLCB1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q9NQ66; -.
ChemistryChEMBL CHEMBL4034; -.
ChemistryBindingDB Q9NQ66; -.
ChemistryChEMBL CHEMBL4034; -.
Organism-specific databasesPharmGKB PA33384; -.
Organism-specific databasesPharmGKB PA33384; -.
Organism-specific databasesCTD 23236; -.
Organism-specific databasesCTD 23236; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00945phospholipase C, beta 1 (phosphoinositide-specific)approvedAcetylsalicylic acid
DB00125phospholipase C, beta 1 (phosphoinositide-specific)approved; nutraceuticalL-Arginine
DB00435phospholipase C, beta 1 (phosphoinositide-specific)approvedNitric Oxide
DB00171phospholipase C, beta 1 (phosphoinositide-specific)approved; nutraceuticalAdenosine triphosphate
DB00988phospholipase C, beta 1 (phosphoinositide-specific)approvedDopamine
DB00917phospholipase C, beta 1 (phosphoinositide-specific)approvedDinoprostone
DB01240phospholipase C, beta 1 (phosphoinositide-specific)approvedEpoprostenol
DB01115phospholipase C, beta 1 (phosphoinositide-specific)approvedNifedipine


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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



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