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 PLCE1
Basic gene info.Gene symbolPLCE1
Gene namephospholipase C, epsilon 1
SynonymsNPHS3|PLCE|PPLC
CytomapUCSC genome browser: 10q23
Genomic locationchr10 :95753745-96088148
Type of geneprotein-coding
RefGenesNM_001165979.2,
NM_001288989.1,NM_016341.3,
Ensembl idENSG00000138193
Description1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase epsilon-1PLC-epsilon-1pancreas-enriched phospholipase Cphosphoinositide phospholipase C-epsilon-1phosphoinositide-specific phospholipase C epsilon-1
Modification date20141207
dbXrefs MIM : 608414
HGNC : HGNC
Ensembl : ENSG00000138193
HPRD : 07087
Vega : OTTHUMG00000018789
ProteinUniProt: Q9P212
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCE1
BioGPS: 51196
Gene Expression Atlas: ENSG00000138193
The Human Protein Atlas: ENSG00000138193
PathwayNCI Pathway Interaction Database: PLCE1
KEGG: PLCE1
REACTOME: PLCE1
ConsensusPathDB
Pathway Commons: PLCE1
MetabolismMetaCyc: PLCE1
HUMANCyc: PLCE1
RegulationEnsembl's Regulation: ENSG00000138193
miRBase: chr10 :95,753,745-96,088,148
TargetScan: NM_001165979
cisRED: ENSG00000138193
ContextiHOP: PLCE1
cancer metabolism search in PubMed: PLCE1
UCL Cancer Institute: PLCE1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PLCE1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLCE1
Familial Cancer Database: PLCE1
* 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

check002.gifOthers
OMIM 608414; gene.
608414; gene.
610725; phenotype.
610725; phenotype.
Orphanet 93213; Familial idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis.
93213; Familial idiopathic steroid-resistant nephrotic syndrome with focal segmental hyalinosis.
93217; Familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis.
93217; Familial idiopathic steroid-resistant nephrotic syndrome with diffuse mesangial sclerosis.
DiseaseKEGG Disease: PLCE1
MedGen: PLCE1 (Human Medical Genetics with Condition)
ClinVar: PLCE1
PhenotypeMGI: PLCE1 (International Mouse Phenotyping Consortium)
PhenomicDB: PLCE1

Mutations for PLCE1
* 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
pancreasPLCE1chr109583717295837192chr109568650495686524
pancreasPLCE1chr109604227796042297PLCE1chr109604329296043312
pancreasPLCE1chr109605663796056657PLCE1chr109606117196061191
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 PLCE1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA374251PLCE11137109579143295791568NEBL138543102107161221072017
AK025366PLCE111724109601136296013085PLCE117182011109600814796008440

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 # sample 1 2  3 1   1    
GAIN (# sample)   2  1          
LOSS (# sample) 1    2 1   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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=153)
Stat. for Synonymous SNVs
(# total SNVs=37)
Stat. for Deletions
(# total SNVs=4)
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
chr10:96030337-96030337p.R1495Q6
chr10:96084175-96084175p.E2191K3
chr10:95790940-95790940p.R46Q3
chr10:95791355-95791355p.R184R3
chr10:96066363-96066363p.V1934V3
chr10:95791100-95791100p.A99A2
chr10:95892028-95892028p.R435K2
chr10:95994038-95994038p.P728Q2
chr10:95791437-95791437p.D212N2
chr10:96018884-96018884p.T1264I2

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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
# sample5124281 13 4 4221331 4518123
# mutation5124331 16 4 4231431 5923142
nonsynonymous SNV3102281 9 3 4161111 4311 33
synonymous SNV2225  7 1  732  1612110
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
chr10:95790940p.D212Y,PLCE13
chr10:96084175p.R46Q,PLCE13
chr10:95791437p.E1883K,PLCE13
chr10:95892039p.R1187Q,PLCE12
chr10:95791949p.L303M,PLCE12
chr10:95987095p.G1921E,PLCE12
chr10:95790955p.T306T,PLCE12
chr10:96030304p.P382P,PLCE12
chr10:95892086p.A99A,PLCE12
chr10:95791574p.S903S,PLCE12

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 PLCE1 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 PLCE1

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

ANKRD36BP1,ARSJ,CADM1,CREB3L2,GREB1L,JMJD1C,KCNQ5,
MAML2,MAP2,OSBPL1A,PLCE1,PPL,PTPN14,SDC2,
SORBS2,SOX6,SLC35G1,TNFSF15,TRPV4,VEPH1,YAP1
ANO6,AVPR1A,CDC42BPA,CRYBG3,KATNAL1,KLHL20,LIMS1,
TENM3___TENM1,PDE3A,PHLDB2,PIK3CA,PLCE1,PLSCR4,PTPRG,
PVRL3,ROCK1,SOX5,SYNE1,TJP1,TMTC1,TTLL7

ABCC13,AHCYL2,ATP11B,B3GALT1,CDHR5,CEACAM7,CNNM4,
ENTPD5,GPA33,HHLA2,ITM2C,MAGI3,MIER3,MOB3B,
MOGAT2,NBEAL1,PDCD4,PLCE1,PLXNA2,SH3RF2,SLC16A9
ABCC3,ATP8B1,PRR14L,CLMN,DNAJC16,FRYL,FZD5,
HIPK2,LARP4B,MAGI3,MAVS,MED14,NBEAL1,PLCE1,
PLEKHA6,PRSS12,RREB1,SATB2,TMEM131,TRPM4,ZDHHC23
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 PLCE1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33391; -.
Organism-specific databasesPharmGKB PA33391; -.
Organism-specific databasesCTD 51196; -.
Organism-specific databasesCTD 51196; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00171phospholipase C, epsilon 1approved; nutraceuticalAdenosine triphosphate
DB00770phospholipase C, epsilon 1approved; investigationalAlprostadil
DB00668phospholipase C, epsilon 1approvedEpinephrine


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Cross referenced IDs for PLCE1
* 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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