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 PRKD1
Basic gene info.Gene symbolPRKD1
Gene nameprotein kinase D1
SynonymsPKC-MU|PKCM|PKD|PRKCM
CytomapUCSC genome browser: 14q11
Genomic locationchr14 :30045686-30396899
Type of geneprotein-coding
RefGenesNM_002742.2,
Ensembl idENSG00000184304
DescriptionnPKC-D1nPKC-muprotein kinase C mu typeprotein kinase C, muprotein kinase Dserine/threonine-protein kinase D1
Modification date20141207
dbXrefs MIM : 605435
HGNC : HGNC
Ensembl : ENSG00000184304
HPRD : 05668
Vega : OTTHUMG00000140203
ProteinUniProt: Q15139
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKD1
BioGPS: 5587
Gene Expression Atlas: ENSG00000184304
The Human Protein Atlas: ENSG00000184304
PathwayNCI Pathway Interaction Database: PRKD1
KEGG: PRKD1
REACTOME: PRKD1
ConsensusPathDB
Pathway Commons: PRKD1
MetabolismMetaCyc: PRKD1
HUMANCyc: PRKD1
RegulationEnsembl's Regulation: ENSG00000184304
miRBase: chr14 :30,045,686-30,396,899
TargetScan: NM_002742
cisRED: ENSG00000184304
ContextiHOP: PRKD1
cancer metabolism search in PubMed: PRKD1
UCL Cancer Institute: PRKD1
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PRKD1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKD1
Familial Cancer Database: PRKD1
* 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
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM 605435; gene.
Orphanet
DiseaseKEGG Disease: PRKD1
MedGen: PRKD1 (Human Medical Genetics with Condition)
ClinVar: PRKD1
PhenotypeMGI: PRKD1 (International Mouse Phenotyping Consortium)
PhenomicDB: PRKD1

Mutations for PRKD1
* 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
ovaryPRKD1chr143026283630262856PRKD1chr143025718830257208
ovaryPRKD1chr143037095530370975PRKD1chr143037127630371296
pancreasPRKD1chr143031327030313470PRKD1chr143031429430314494
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 PRKD1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW580521PRKD13762143021667430216702WAC59175102889722728897605

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 # sample4       9 1   11 
GAIN (# sample)4       8 1   11 
LOSS (# sample)        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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=138)
Stat. for Synonymous SNVs
(# total SNVs=37)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr14:30068249-30068249p.A717V4
chr14:30066795-30066795p.G779D3
chr14:30068938-30068938p.G664V3
chr14:30194796-30194796p.V117M3
chr14:30046613-30046613p.E857G3
chr14:30135363-30135363p.H152R3
chr14:30132965-30132965p.V212V3
chr14:30046614-30046614p.E857*3
chr14:30068238-30068238p.P721S3
chr14:30133009-30133009p.G198C2

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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 301 16 4 119136  517314
# mutation41 321 16 4 121146  519315
nonsynonymous SNV21 241 10 4  17113  31339
synonymous SNV2  9  6   1433  26 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
chr14:30046613p.E857G3
chr14:30100144p.A717V2
chr14:30068938p.T458I2
chr14:30068249p.D841D2
chr14:30105555p.G254A2
chr14:30066890p.N377N2
chr14:30102094p.P747P2
chr14:30108046p.G664V2
chr14:30046660p.F492F2
chr14:30108094p.L406I1

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 PRKD1 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 PRKD1

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

C14orf37,CACNG5,CBLN1,CHSY3,CRYBA2,DCN,DPYSL3,
FEV,GLT8D2,INSRR,KIAA1614,MRVI1,MSRB3,NAP1L3,
PRKD1,RECK,SAMD14,ST8SIA3,TRPM3,TSHZ3,WNT16
BBS7,BNIP2,C4orf3,CLDND1,CLIC4,DPYD,FBXO33,
FBXO8,GNG12,KDSR,LMBRD1,MBNL2,MMGT1,PLEKHA3,
PPP2CB,PRKD1,PTPN12,RAB28,TMEM47,TRPC1,VPS26A

AMOTL1,ARHGEF17,BNC2,CALD1,CYS1,DPYSL3,DZIP1,
FAM110B,FBXL7,FERMT2,JAM3,KANK2,LAYN,MAP1A,
MPDZ,MRVI1,MSRB3,PRKD1,SGCD,STON1,ZEB1
CACNA2D1,CLIP4,COPZ2,DENND5A,EHBP1,FIBIN,GUCY1A3,
KLHL5,LOC344595,PBX3,PHLDB2,PRDM8,PRKD1,RIMKLB,
SCN7A,SULF1,TCEAL3,TCEAL4,WWC2,ZCCHC24,ZEB1
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 PRKD1


There's no related Drug.
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Cross referenced IDs for PRKD1
* 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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