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 PLCD4
Basic gene info.Gene symbolPLCD4
Gene namephospholipase C, delta 4
Synonyms-
CytomapUCSC genome browser: 2q35
Genomic locationchr2 :219472487-219501909
Type of geneprotein-coding
RefGenesNM_032726.3,
Ensembl idENSG00000115556
Description1-phosphatidylinositol 4,5-bisphosphate phosphodiesterase delta-41-phosphatidylinositol-4,5-bisphosphate phosphodiesterase delta-4PLC delta4phosphoinositide phospholipase C-delta-4
Modification date20141207
dbXrefs MIM : 605939
HGNC : HGNC
Ensembl : ENSG00000115556
HPRD : 07296
Vega : OTTHUMG00000154743
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PLCD4
BioGPS: 84812
Gene Expression Atlas: ENSG00000115556
The Human Protein Atlas: ENSG00000115556
PathwayNCI Pathway Interaction Database: PLCD4
KEGG: PLCD4
REACTOME: PLCD4
ConsensusPathDB
Pathway Commons: PLCD4
MetabolismMetaCyc: PLCD4
HUMANCyc: PLCD4
RegulationEnsembl's Regulation: ENSG00000115556
miRBase: chr2 :219,472,487-219,501,909
TargetScan: NM_032726
cisRED: ENSG00000115556
ContextiHOP: PLCD4
cancer metabolism search in PubMed: PLCD4
UCL Cancer Institute: PLCD4
Assigned class in ccmGDBC

Top
Phenotypic Information for PLCD4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PLCD4
Familial Cancer Database: PLCD4
* 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
Orphanet
DiseaseKEGG Disease: PLCD4
MedGen: PLCD4 (Human Medical Genetics with Condition)
ClinVar: PLCD4
PhenotypeMGI: PLCD4 (International Mouse Phenotyping Consortium)
PhenomicDB: PLCD4

Mutations for PLCD4
* 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
ovaryPLCD4chr2219492269219492289chr2218124122218124142
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 PLCD4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ183357ARF1195121228286417228286910PLCD45106902219500615219501106
BX102201PLCD414102219488760219489169MARC24075121220932026220932131
CV404934XXYLT1101483194878771194878912PLCD41452172219498978219499050

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1             1  
GAIN (# sample)1             1  
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
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=2

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=45)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr2:219487409-219487409p.E194*3
chr2:219486299-219486299p.E173*2
chr2:219499340-219499340p.T628N2
chr2:219480467-219480467p.A2V2
chr2:219496970-219496970p.E462K1
chr2:219492760-219492760p.R261W1
chr2:219498885-219498885p.L555P1
chr2:219480782-219480782p.S60G1
chr2:219494296-219494296p.S343R1
chr2:219500990-219500990p.T686K1

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32 4  2 3  633 15218
# mutation32 4  2 3  633 172110
nonsynonymous SNV21 3  2 2  4 3 13118
synonymous SNV11 1    1  23   41 2
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
chr2:219498867p.R549H2
chr2:219480467p.G55D1
chr2:219487534p.S343R1
chr2:219501078p.L555P1
chr2:219496889p.N71T1
chr2:219480768p.G351R1
chr2:219498885p.G597G1
chr2:219487535p.E83E1
chr2:219501103p.V364A1
chr2:219496958p.Q612Q1

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 PLCD4 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 PLCD4

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

ABCA2,AFF3,ASB16,C8orf86,CACNA2D2,COQ10A,DNAJC12,
DNALI1,FAM57B,GATA3,ICA1L,INPP5J,KCTD6,CCDC183,
LYPD6B,MAP3K12,NEURL1,P4HTM,PLCD4,RELL1,SEMA3F
RBFOX1,ASB16,MLIP,CA3,CACNG1,CALML6,CKMT2,
CLCN1,CMYA5,CTNNA3,FBXO40,MYH1,MYH7B,MYOZ3,
PGAM2,PKIA,PLCD4,PYGM,SLC25A4,SLC36A2,TMEM38A

APOBEC2,ASTN1,ATCAY,ATP2B3,DKFZP434L187,DPYSL5,GPR26,
GRIN2A,IGSF11,JPH4,LOC200726,NRXN1,PCSK2,PLCD4,
RPRM,SCN1A,SLC7A14,SYT6,THSD7B,TMEM59L,UNC80
ASIC1,ATP1A2,ATP2B4,BVES,CA14,CACNA1H,DACT3,
KCNH2,KY,LDB3,MPP2,NPTXR,NRXN2,PLCD4,
PTGS1,PYGM,SLC8A2,SMTN,SPEG,TACR2,TGFB1I1
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 PLCD4


There's no related Drug.
Top
Cross referenced IDs for PLCD4
* 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