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 PRKCD
Basic gene info.Gene symbolPRKCD
Gene nameprotein kinase C, delta
SynonymsALPS3|CVID9|MAY1|PKCD|nPKC-delta
CytomapUCSC genome browser: 3p21.31
Genomic locationchr3 :53195222-53226733
Type of geneprotein-coding
RefGenesNM_006254.3,
NM_212539.1,
Ensembl idENSG00000163932
Descriptionprotein kinase C delta VIIIprotein kinase C delta typetyrosine-protein kinase PRKCD
Modification date20141222
dbXrefs MIM : 176977
HGNC : HGNC
Ensembl : ENSG00000163932
HPRD : 01501
Vega : OTTHUMG00000133659
ProteinUniProt: Q05655
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKCD
BioGPS: 5580
Gene Expression Atlas: ENSG00000163932
The Human Protein Atlas: ENSG00000163932
PathwayNCI Pathway Interaction Database: PRKCD
KEGG: PRKCD
REACTOME: PRKCD
ConsensusPathDB
Pathway Commons: PRKCD
MetabolismMetaCyc: PRKCD
HUMANCyc: PRKCD
RegulationEnsembl's Regulation: ENSG00000163932
miRBase: chr3 :53,195,222-53,226,733
TargetScan: NM_006254
cisRED: ENSG00000163932
ContextiHOP: PRKCD
cancer metabolism search in PubMed: PRKCD
UCL Cancer Institute: PRKCD
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 176977; gene.
615559; phenotype.
Orphanet 1572; Common variable immunodeficiency.
300345; Autosomal recessive systemic lupus erythematosus.
3261; Autoimmune lymphoproliferative syndrome.
DiseaseKEGG Disease: PRKCD
MedGen: PRKCD (Human Medical Genetics with Condition)
ClinVar: PRKCD
PhenotypeMGI: PRKCD (International Mouse Phenotyping Consortium)
PhenomicDB: PRKCD

Mutations for PRKCD
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PRKCD related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CA309863PRKCD248735322618153226668TFIP11480648222690277026906073
BG982322PVRL11714211119535513119535640PRKCD13227735322281453223159
AI457515PRKCD328035322645853226733PRKCD27558835321718253219666
BI021268PRKCD123135321912353219353TBC1D82214902101700156101700425
AK130023PRKCD72178535322451453226919PRKCD1779204135322639153226653

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        2 1      
GAIN (# sample)        2 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)

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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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=39)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr3:53219628-53219628p.S299S3
chr3:53220653-53220653p.D434fs*23
chr3:53212455-53212455p.R6H3
chr3:53213676-53213676p.R67S3
chr3:53226261-53226261p.F670F2
chr3:53223221-53223221p.P568S2
chr3:53212542-53212542p.A35V2
chr3:53220215-53220215p.E373E2
chr3:53212456-53212456p.R6R2
chr3:53223177-53223177p.E553G2

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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
# sample41 154 1 6  32   66 8
# mutation41 134 1 5  32   76 10
nonsynonymous SNV11 91 1 3  32   36 7
synonymous SNV3  43   2       4  3
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
chr3:53213676p.R67C,PRKCD4
chr3:53217202p.R6R,PRKCD2
chr3:53212542p.F670F,PRKCD2
chr3:53226261p.A35V,PRKCD2
chr3:53223177p.S299S,PRKCD2
chr3:53219628p.E553G,PRKCD2
chr3:53212456p.A213T,PRKCD2
chr3:53219979p.V235V,PRKCD1
chr3:53222823p.L481L,PRKCD1
chr3:53212512p.L610V,PRKCD1

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 PRKCD 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 PRKCD

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

APEH,ARF3,ARSG,HID1,CCDC51,CYB561D2,DALRD3,
FOXA1,GPRC5A,HIST2H4A,KCTD6,NME6,NPRL2,PDHB,
PRKCD,QRICH1,RNF123,SEMA3F,SPCS1,TMBIM6,TUSC2
AIFM2,AKR1C2,ANXA5,BTD,DHDDS,ELMOD3,EPHX1,
FADS3,ITIH5,ITPK1,MRAP,MRAS,PHLDB1,PLXNA4,
PMEPA1,PRKCD,PYGL,RETSAT,TFE3,TK2,VKORC1L1

BCAS1,C11orf86,C1orf94,CACFD1,CDHR5,CIDEC,CLDN23,
DHRS9,GLRA4,IL17RE,FAM214B,LOC646627,MGLL,MYPN,
PLA2G10,PRKCD,PRSS8,TMEM82,TRANK1,UGT1A4,VSIG1
APPL2,C1orf106,C2CD2L,CGN,CTSZ,DOK4,HECTD3,
HHLA2,KIAA0247,LASP1,MAST2,MYO15B,PLEKHG6,PRKCD,
SPINT1,TAOK3,TJP3,TRIM36,VDR,VILL,ZBTB7B
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 PRKCD
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q05655; -.
ChemistryChEMBL CHEMBL2093867; -.
ChemistryGuidetoPHARMACOLOGY 1485; -.
Organism-specific databasesPharmGKB PA33763; -.
Organism-specific databasesCTD 5580; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB04376protein kinase C, deltaexperimental13-Acetylphorbol
DB01394protein kinase C, deltaapprovedColchicine
DB00988protein kinase C, deltaapprovedDopamine
DB00143protein kinase C, deltaapproved; nutraceuticalGlutathione
DB00125protein kinase C, deltaapproved; nutraceuticalL-Arginine
DB00435protein kinase C, deltaapprovedNitric Oxide
DB00864protein kinase C, deltaapproved; investigationalTacrolimus


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Cross referenced IDs for PRKCD
* 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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