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 symbolPLCG1
Gene namephospholipase C, gamma 1
SynonymsNCKAP3|PLC-II|PLC1|PLC148|PLCgamma1
CytomapUCSC genome browser: 20q12-q13.1
Genomic locationchr20 :39766160-39804357
Type of geneprotein-coding
RefGenesNM_002660.2,
NM_182811.1,
Ensembl idENSG00000124181
Description1-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 date20141207
dbXrefs MIM : 172420
HGNC : HGNC
Ensembl : ENSG00000124181
HPRD : 01398
Vega : OTTHUMG00000033082
ProteinUniProt: P19174
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCG1
BioGPS: 5335
Gene Expression Atlas: ENSG00000124181
The Human Protein Atlas: ENSG00000124181
PathwayNCI Pathway Interaction Database: PLCG1
KEGG: PLCG1
REACTOME: PLCG1
ConsensusPathDB
Pathway Commons: PLCG1
MetabolismMetaCyc: PLCG1
HUMANCyc: PLCG1
RegulationEnsembl's Regulation: ENSG00000124181
miRBase: chr20 :39,766,160-39,804,357
TargetScan: NM_002660
cisRED: ENSG00000124181
ContextiHOP: PLCG1
cancer metabolism search in PubMed: PLCG1
UCL Cancer Institute: PLCG1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLCG1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_INOSITOL_PHOSPHATE_METABOLISM
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS

check002.gifOthers
OMIM 172420; gene.
Orphanet
DiseaseKEGG Disease: PLCG1
MedGen: PLCG1 (Human Medical Genetics with Condition)
ClinVar: PLCG1
PhenotypeMGI: PLCG1 (International Mouse Phenotyping Consortium)
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.

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
pancreasPLCG1chr203977170139771721TMEM104chr177278216672782186
pancreasPLCG1chr203979638339796403PLCG1chr203977195739771977
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 PLCG1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CK724856PLCG119180203980419839804359FRMD8178666116516427265168339
BI014551MYH1414278195081189450812157PLCG1271417203979911639799262
AA018565ZBTB22183645144414514523PLCG166412203979532939797506
BF770556ARID1B63016157110928157111227PLCG1298509203979924539799456
AW894554ZEB2141892145271641145271818PLCG1184355203980084939801151

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 # sample1     2          
GAIN (# sample)1     2          
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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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=9

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check002.gifSomatic 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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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
chr20:39792584-39792584p.S345F9
chr20:39795235-39795235p.R707Q6
chr20:39793963-39793963p.S489P3
chr20:39802384-39802384p.E1163K3
chr20:39802942-39802942p.R1275Q3
chr20:39794432-39794432p.E589Q2
chr20:39802848-39802848p.R1244*2
chr20:39801087-39801087p.R978W2
chr20:39801100-39801100p.S982F2
chr20:39802889-39802889p.P1257P2

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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
# sample471244 513  771  1516 17
# mutation471225 513  771  1617 18
nonsynonymous SNV45 135 51   741  914 12
synonymous SNV 219    3   3   73 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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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
chr20:39798904p.E1163K,PLCG13
chr20:39802384p.S489P,PLCG13
chr20:39793963p.A935T,PLCG13
chr20:39802942p.R978W,PLCG12
chr20:39792036p.E809K,PLCG12
chr20:39794395p.S489S,PLCG12
chr20:39797452p.R1275Q,PLCG12
chr20:39788351p.V108A,PLCG12
chr20:39793965p.F731F,PLCG12
chr20:39801087p.R270C,PLCG12

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 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

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

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
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 PLCG1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P19174; -.
ChemistryChEMBL CHEMBL3964; -.
Organism-specific databasesPharmGKB PA33392; -.
Organism-specific databasesCTD 5335; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171phospholipase C, gamma 1approved; nutraceuticalAdenosine triphosphate
DB00131phospholipase C, gamma 1approved; nutraceuticalAdenosine monophosphate
DB00125phospholipase C, gamma 1approved; nutraceuticalL-Arginine
DB00155phospholipase C, gamma 1approved; nutraceuticalL-Citrulline
DB00435phospholipase C, gamma 1approvedNitric Oxide
DB00608phospholipase C, gamma 1approvedChloroquine
DB00864phospholipase C, gamma 1approved; investigationalTacrolimus


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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



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