Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 PLCD1
Basic gene info.Gene symbolPLCD1
Gene namephospholipase C, delta 1
SynonymsNDNC3|PLC-III
CytomapUCSC genome browser: 3p22-p21.3
Genomic locationchr3 :38048986-38066278
Type of geneprotein-coding
RefGenesNM_001130964.1,
NM_006225.3,NR_024071.1,
Ensembl idENSG00000187091
Description1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-11-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-1PLC-delta-1phosphoinositide phospholipase C-delta-1phospholipase C-III
Modification date20141207
dbXrefs MIM : 602142
HGNC : HGNC
Ensembl : ENSG00000187091
HPRD : 09073
Vega : OTTHUMG00000130813
ProteinUniProt: P51178
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCD1
BioGPS: 5333
Gene Expression Atlas: ENSG00000187091
The Human Protein Atlas: ENSG00000187091
PathwayNCI Pathway Interaction Database: PLCD1
KEGG: PLCD1
REACTOME: PLCD1
ConsensusPathDB
Pathway Commons: PLCD1
MetabolismMetaCyc: PLCD1
HUMANCyc: PLCD1
RegulationEnsembl's Regulation: ENSG00000187091
miRBase: chr3 :38,048,986-38,066,278
TargetScan: NM_001130964
cisRED: ENSG00000187091
ContextiHOP: PLCD1
cancer metabolism search in PubMed: PLCD1
UCL Cancer Institute: PLCD1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PLCD1 in cancer cell metabolism1. Xiang T, Li L, Fan Y, Jiang Y, Ying Y, et al. (2010) PLCD1 is a functional tumor suppressor inducing G2/M arrest and frequently methylated in breast cancer. Cancer biology & therapy 10: 520-527. go to article

Top
Phenotypic Information for PLCD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLCD1
Familial Cancer Database: PLCD1
* 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 151600; phenotype.
602142; gene.
Orphanet 2387; Leukonychia totalis.
DiseaseKEGG Disease: PLCD1
MedGen: PLCD1 (Human Medical Genetics with Condition)
ClinVar: PLCD1
PhenotypeMGI: PLCD1 (International Mouse Phenotyping Consortium)
PhenomicDB: PLCD1

Mutations for PLCD1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PLCD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CN404773INS-IGF211111121538872153997PLCD19418533805350538246281

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=44)
Stat. for Synonymous SNVs
(# total SNVs=19)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

Top
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
chr3:38052853-38052853p.I214I4
chr3:38061700-38061700p.R60W3
chr3:38058047-38058047p.W121*2
chr3:38050789-38050789p.R527H2
chr3:38051251-38051251p.P447A2
chr3:38051941-38051941p.P301P2
chr3:38050127-38050127p.V575G1
chr3:38052015-38052015p.M277V1
chr3:38051179-38051179p.E471*1
chr3:38053064-38053064p.D177N1

Top
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
# sample11 123 2 21 52   45111
# mutation11 123 2 21 62   55111
nonsynonymous SNV1  103 2 21 51   4416
synonymous SNV 1 2       11   11 5
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
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
chr3:38061700p.R81W,PLCD13
chr3:38052853p.I235I,PLCD13
chr3:38050888p.R61H,PLCD12
chr3:38049554p.K733N,PLCD12
chr3:38061759p.D515G,PLCD12
chr3:38050579p.N668K,PLCD11
chr3:38065845p.E485K,PLCD11
chr3:38051649p.R159H,PLCD11
chr3:38053094p.K667N,PLCD11
chr3:38049815p.A477A,PLCD11

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 PLCD1 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 PLCD1

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))
Top
check002.gifCNV 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
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

ACAN,C16orf90,C4orf51,PXDC1,DSG3,EXTL1,FES,
FXYD6,KCNG1,KLK8,MFGE8,PGM5P2,PLCD1,PMP2,
RNF222,SLC15A1,SPEG,TFEB,TRPV4,VILL,ZBTB32
B3GALT4,CTDSP1,DDAH2,EML3,HYI,INF2,KIFC3,
KLHL22,LMF2,LOC729991,LRP3,MMP24,MXD4,NUCB1,
PLCD1,SNX17,TMEM129,TSPAN15,UCK1,UROD,WTIP

ABTB1,B3GALT4,BTD,CACFD1,CAPN5,FBXW5,IL17RC,
KIAA0513,MGLL,PDCD4,PLCD1,PNPLA2,PNPLA7,PRKCD,
SERINC2,TMEM115,TMEM59,VIPR1,VSIG2,YPEL3,ZER1
ABHD3,AHCYL2,AMACR,CA4,CAPN2,CLCN2,ENPP1,
GBA,LIPH,LITAF,MGLL,MKRN1,PEX26,PLCD1,
PRDX6,SCNN1A,SLC26A3,SLC4A4,SPATS2L,TJP3,TMEM63B
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

Top
check002.gifInteracting Genes (from Pathway Commons)

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

Top
Pharmacological Information for PLCD1


There's no related Drug.
Top
Cross referenced IDs for PLCD1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas