Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 symbol	PLCG2
	Gene name	phospholipase C, gamma 2 (phosphatidylinositol-specific)
	Synonyms	APLAID\|FCAS3\|PLC-IV\|PLC-gamma-2
	Cytomap	UCSC genome browser: 16q24.1
	Genomic location	chr16 :81812898-81991899
	Type of gene	protein-coding
	RefGenes	NM_002661.4,
	Ensembl id	ENSG00000197943
	Description	1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-2phosphoinositide phospholipase C-gamma-2phospholipase C-IV
	Modification date	20141207
dbXrefs	MIM : 600220
	HGNC : HGNC
	Ensembl : ENSG00000197943
	Ensembl : ENSG00000261218
	HPRD : 02570
Protein	UniProt: P16885 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCG2
	BioGPS: 5336
	Gene Expression Atlas: ENSG00000197943
	The Human Protein Atlas: ENSG00000197943
Pathway	NCI Pathway Interaction Database: PLCG2
	KEGG: PLCG2
	REACTOME: PLCG2
	ConsensusPathDB
	Pathway Commons: PLCG2
Metabolism	MetaCyc: PLCG2
	HUMANCyc: PLCG2
Regulation	Ensembl's Regulation: ENSG00000197943
	miRBase: chr16 :81,812,898-81,991,899
	TargetScan: NM_002661
	cisRED: ENSG00000197943
Context	iHOP: PLCG2
	cancer metabolism search in PubMed: PLCG2
	UCL Cancer Institute: PLCG2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

Top

Phenotypic Information for PLCG2(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS

Others
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.
Disease	KEGG Disease: PLCG2
	MedGen: PLCG2 (Human Medical Genetics with Condition)
	ClinVar: PLCG2
Phenotype	MGI: PLCG2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

Top

- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PLCG2	chr16	81934762	81934782	PLCG2	chr16	81940434	81940454

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 PLCG2 related fusion information.

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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=4

Top

Somatic 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)

Top

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
chr16:81934316-81934316	p.T431T	4
chr16:81934352-81934352	p.S443S	3
chr16:81944272-81944272	p.F627F	3
chr16:81902829-81902829	p.R164*	3
chr16:81968079-81968079	p.E929K	3
chr16:81942093-81942093	p.E544K	3
chr16:81954830-81954830	p.V755I	2
chr16:81941355-81941355	p.Q511H	2
chr16:81979857-81979857	p.R1187W	2
chr16:81953214-81953214	p.R727Q	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	4	4	3	18	7		6		2	2		12	6	2		2	24	14	1	23
# mutation	4	4	3	20	7		6		2	2		13	7	2		2	36	17	1	35
nonsynonymous SNV	2	3	3	15	3		3		1	2		9	6	1		1	21	10	1	27
synonymous SNV	2	1		5	4		3		1			4	1	1		1	15	7		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])

Top

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
chr16:81934316	p.F627F	3
chr16:81968079	p.T431T	3
chr16:81944272	p.E929K	3
chr16:81927341	p.P1083S	2
chr16:81819622	p.L10I	2
chr16:81934352	p.V755I	2
chr16:81954830	p.E544K	2
chr16:81942093	p.S443S	2
chr16:81972454	p.D81N	2
chr16:81969848	p.D973N	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 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]

Top

Gene Expression for PLCG2

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for PLCG2

There's no related Drug.

Top

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