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 PLCG2
Basic gene info.Gene symbolPLCG2
Gene namephospholipase C, gamma 2 (phosphatidylinositol-specific)
SynonymsAPLAID|FCAS3|PLC-IV|PLC-gamma-2
CytomapUCSC genome browser: 16q24.1
Genomic locationchr16 :81812898-81991899
Type of geneprotein-coding
RefGenesNM_002661.4,
Ensembl idENSG00000197943
Description1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2phosphoinositide phospholipase C-gamma-2phospholipase C-IV
Modification date20141207
dbXrefs MIM : 600220
HGNC : HGNC
Ensembl : ENSG00000197943
Ensembl : ENSG00000261218
HPRD : 02570
ProteinUniProt: P16885
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCG2
BioGPS: 5336
Gene Expression Atlas: ENSG00000197943
The Human Protein Atlas: ENSG00000197943
PathwayNCI Pathway Interaction Database: PLCG2
KEGG: PLCG2
REACTOME: PLCG2
ConsensusPathDB
Pathway Commons: PLCG2
MetabolismMetaCyc: PLCG2
HUMANCyc: PLCG2
RegulationEnsembl's Regulation: ENSG00000197943
miRBase: chr16 :81,812,898-81,991,899
TargetScan: NM_002661
cisRED: ENSG00000197943
ContextiHOP: PLCG2
cancer metabolism search in PubMed: PLCG2
UCL Cancer Institute: PLCG2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLCG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLCG2
Familial Cancer Database: PLCG2
* 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
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS

check002.gifOthers
OMIM 600220; gene.
614468; phenotype.
614878; phenotype.
Orphanet 300359; PLCG2-associated antibody deficiency and immune dysregulation.
324530; Autoinflammation and PLCG2-associated antibody deficiency and immune dysregulation.
DiseaseKEGG Disease: PLCG2
MedGen: PLCG2 (Human Medical Genetics with Condition)
ClinVar: PLCG2
PhenotypeMGI: PLCG2 (International Mouse Phenotyping Consortium)
PhenomicDB: PLCG2

Mutations for PLCG2
* 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
ovaryPLCG2chr168193476281934782PLCG2chr168194043481940454
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 PLCG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample2  1    1        
GAIN (# sample)   1             
LOSS (# sample)2       1        
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=130)
Stat. for Synonymous SNVs
(# total SNVs=40)
Stat. for Deletions
(# total SNVs=4)
Stat. for Insertions
(# total SNVs=1)

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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
chr16:81934316-81934316p.T431T4
chr16:81944272-81944272p.F627F3
chr16:81902829-81902829p.R164*3
chr16:81968079-81968079p.E929K3
chr16:81942093-81942093p.E544K3
chr16:81934352-81934352p.S443S3
chr16:81929430-81929430p.P364H2
chr16:81888096-81888096p.D81Y2
chr16:81904518-81904518p.L209H2
chr16:81969848-81969848p.D973N2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample443187 6 22 1262 22414123
# mutation443207 6 22 1372 23617135
nonsynonymous SNV233153 3 12 961 12110127
synonymous SNV21 54 3 1  411 1157 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
chr16:81944272p.F627F3
chr16:81934316p.T431T3
chr16:81968079p.E929K3
chr16:81942093p.D973N2
chr16:81972454p.S338S2
chr16:81969848p.Q511H2
chr16:81941355p.P1083S2
chr16:81888096p.L10I2
chr16:81927341p.V755I2
chr16:81819622p.E544K2

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 PLCG2 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 PLCG2

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

BBOX1,KIAA0226L,CA6,CCDC82,CMTM7,FAM49A,GABRP,
HAPLN3,HLA-DOB,IFNAR2,INPP5D,LYN,MLKL,PLCG2,
PRKX,RCSD1,SEL1L3,SH3KBP1,TAGAP,TRAF3IP3,TSPAN33
ADD2,AKNA,ARHGAP25,ARHGAP9,BIN2,CIITA,CSF2RB,
GZMB,IL12RB1,IL18R1,IL2RB,KIF21B,LCP2,LRMP,
NLRC5,P2RY8,PIK3CD,PLCG2,PRF1,PTK2B,TMC8

ARHGAP25,BTK,CD37,DOCK2,IKZF1,IL16,TESPA1,
KLHL6,LY9,MAP4K1,P2RY8,PIK3CD,PLCG2,POU2F2,
PPP1R16B,PRKCB,PTPRC,RCSD1,SASH3,WDFY4,ZNF831
BEND4,NUGGC,CD79A,CYFIP2,DOCK8,DOK3,DTX1,
IGLL1,INPP5D,KCNK12,KLHL6,LRMP,NUP210,P2RY8,
PIK3CG,PLCG2,POU2AF1,RFTN1,SH2B2,TLR9,WDFY4
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 PLCG2


There's no related Drug.
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Cross referenced IDs for PLCG2
* 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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