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

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 PLCG1

Basic gene info.	Gene symbol	PLCG1
	Gene name	phospholipase C, gamma 1
	Synonyms	NCKAP3\|PLC-II\|PLC1\|PLC148\|PLCgamma1
	Cytomap	UCSC genome browser: 20q12-q13.1
	Genomic location	chr20 :39766160-39804357
	Type of gene	protein-coding
	RefGenes	NM_002660.2, NM_182811.1,
	Ensembl id	ENSG00000124181
	Description	1-phosphatidyl-D-myo-inositol-4,5-bisphosphate1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase gamma-11-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma 11-phosphatidylinositol-4,5-bisphosphate phosphodiesterase gamma-1PLC-148PL
	Modification date	20141207
dbXrefs	MIM : 172420
	HGNC : HGNC
	Ensembl : ENSG00000124181
	HPRD : 01398
	Vega : OTTHUMG00000033082
Protein	UniProt: P19174 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PLCG1
	BioGPS: 5335
	Gene Expression Atlas: ENSG00000124181
	The Human Protein Atlas: ENSG00000124181
Pathway	NCI Pathway Interaction Database: PLCG1
	KEGG: PLCG1
	REACTOME: PLCG1
	ConsensusPathDB
	Pathway Commons: PLCG1
Metabolism	MetaCyc: PLCG1
	HUMANCyc: PLCG1
Regulation	Ensembl's Regulation: ENSG00000124181
	miRBase: chr20 :39,766,160-39,804,357
	TargetScan: NM_002660
	cisRED: ENSG00000124181
Context	iHOP: PLCG1
	cancer metabolism search in PubMed: PLCG1
	UCL Cancer Institute: PLCG1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PLCG1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PLCG1
	Familial Cancer Database: PLCG1

* 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 GBM ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nejm.org/doi/full/10.1056/NEJMoa1402121,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

Metabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS

Others
OMIM	172420; gene.
Orphanet
Disease	KEGG Disease: PLCG1
	MedGen: PLCG1 (Human Medical Genetics with Condition)
	ClinVar: PLCG1
Phenotype	MGI: PLCG1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PLCG1

Mutations for PLCG1

* 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

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	PLCG1	chr20	39771701	39771721	TMEM104	chr17	72782166	72782186
pancreas	PLCG1	chr20	39796383	39796403	PLCG1	chr20	39771957	39771977

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 PLCG1 related fusion information.

ID	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
CK724856	PLCG1	19	180	20	39804198	39804359	FRMD8	178	666	11	65164272	65168339
BI014551	MYH14	14	278	19	50811894	50812157	PLCG1	271	417	20	39799116	39799262
AA018565	ZBTB22	1	83	6	4514441	4514523	PLCG1	66	412	20	39795329	39797506
BF770556	ARID1B	6	301	6	157110928	157111227	PLCG1	298	509	20	39799245	39799456
AW894554	ZEB2	14	189	2	145271641	145271818	PLCG1	184	355	20	39800849	39801151

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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)

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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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=108)	Stat. for Synonymous SNVs (# total SNVs=36)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr20:39792584-39792584	p.S345F	9
chr20:39795235-39795235	p.R707Q	6
chr20:39793963-39793963	p.S489P	3
chr20:39802384-39802384	p.E1163K	3
chr20:39802942-39802942	p.R1275Q	3
chr20:39794432-39794432	p.E589Q	2
chr20:39802848-39802848	p.R1244*	2
chr20:39801087-39801087	p.R978W	2
chr20:39801100-39801100	p.S982F	2
chr20:39802889-39802889	p.P1257P	2

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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	7	1	24	4		5	1	3			7	7	1			15	16		17
# mutation	4	7	1	22	5		5	1	3			7	7	1			16	17		18
nonsynonymous SNV	4	5		13	5		5	1				7	4	1			9	14		12
synonymous SNV		2	1	9					3				3				7	3		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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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
chr20:39798904	p.E1163K,PLCG1	3
chr20:39802384	p.S489P,PLCG1	3
chr20:39793963	p.A935T,PLCG1	3
chr20:39802942	p.E809K,PLCG1	2
chr20:39792036	p.S489S,PLCG1	2
chr20:39794395	p.R1275Q,PLCG1	2
chr20:39797452	p.V108A,PLCG1	2
chr20:39788351	p.F731F,PLCG1	2
chr20:39793965	p.R270C,PLCG1	2
chr20:39801087	p.T576T,PLCG1	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 PLCG1 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 PLCG1

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))

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CNV 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

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


CABLES2,CCDC142,DHX35,DLGAP4,DNMT3A,DNMT3B,GPC2, KCNAB3,LPIN3,LY6G5B,NINL,PLCG1,RTEL1,SS18L1, TGIF2,TOP1P1,UCKL1,ZBTB46,ZCCHC18,ZNF335,ZNF512B	ABCA2,ANKRD11,ARHGEF11,ARHGEF17,PRRC2B,BCL9L,CEP250, CMTR1,KIRREL,KLHL36,MED12,PLCG1,PRICKLE4,SIN3B, SUPT6H,TECPR1,TNPO2,TRIM56,ZBTB46,ZC3H7B,ZNF646

ASXL1,NOL4L,CBFA2T2,CEP250,CHD6,DHX35,DIDO1, ELMO2,TTI1,KIF3B,LOC647979,NCOA6,PLCG1,RALGAPB, RBM39,SNORA71E,SS18L1,STX16,TRPC4AP,ZGPAT,ZNF335	ASAP1,ASXL1,PRRC2B,CHD6,CLCN6,FAM193A,PIEZO1, HERC1,IQSEC1,LZTR1,KMT2A,OBSCN,PHF12,PHF2, PLCG1,POGZ,TNRC6A,TRERF1,ZNF37BP,ZNF516,ZNF589

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

: Open all plots for all cancer types

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Interacting 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 PLCG1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P19174; -.
Chemistry	ChEMBL	CHEMBL3964; -.
Organism-specific databases	PharmGKB	PA33392; -.
Organism-specific databases	CTD	5335; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00171	phospholipase C, gamma 1	approved; nutraceutical	Adenosine triphosphate
DB00131	phospholipase C, gamma 1	approved; nutraceutical	Adenosine monophosphate
DB00125	phospholipase C, gamma 1	approved; nutraceutical	L-Arginine
DB00155	phospholipase C, gamma 1	approved; nutraceutical	L-Citrulline
DB00435	phospholipase C, gamma 1	approved	Nitric Oxide
DB00608	phospholipase C, gamma 1	approved	Chloroquine
DB00864	phospholipase C, gamma 1	approved; investigational	Tacrolimus

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Cross referenced IDs for PLCG1

* 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