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 PRKCA
Basic gene info.Gene symbolPRKCA
Gene nameprotein kinase C, alpha
SynonymsAAG6|PKC-alpha|PKCA|PRKACA
CytomapUCSC genome browser: 17q22-q23.2
Genomic locationchr17 :64298925-64806862
Type of geneprotein-coding
RefGenesNM_002737.2,
Ensembl idENSG00000154229
DescriptionPKC-Aaging-associated gene 6protein kinase C alpha type
Modification date20141222
dbXrefs MIM : 176960
HGNC : HGNC
Ensembl : ENSG00000154229
HPRD : 01498
Vega : OTTHUMG00000179533
ProteinUniProt: P17252
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKCA
BioGPS: 5578
Gene Expression Atlas: ENSG00000154229
The Human Protein Atlas: ENSG00000154229
PathwayNCI Pathway Interaction Database: PRKCA
KEGG: PRKCA
REACTOME: PRKCA
ConsensusPathDB
Pathway Commons: PRKCA
MetabolismMetaCyc: PRKCA
HUMANCyc: PRKCA
RegulationEnsembl's Regulation: ENSG00000154229
miRBase: chr17 :64,298,925-64,806,862
TargetScan: NM_002737
cisRED: ENSG00000154229
ContextiHOP: PRKCA
cancer metabolism search in PubMed: PRKCA
UCL Cancer Institute: PRKCA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

check002.gifOthers
OMIM 176960; gene.
Orphanet
DiseaseKEGG Disease: PRKCA
MedGen: PRKCA (Human Medical Genetics with Condition)
ClinVar: PRKCA
PhenotypeMGI: PRKCA (International Mouse Phenotyping Consortium)
PhenomicDB: PRKCA

Mutations for PRKCA
* 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
breastPRKCAchr176442656364426563CARD14chr177817307378173073
NSPRKCAchr176462576064625760SDK2chr177143320271433202
ovaryPRKCAchr176432321164323231PRKCAchr176432933564329355
ovaryPRKCAchr176443102364431043PRKCAchr176443998564440005
ovaryPRKCAchr176458596764585987PRKCAchr176458978464589804
ovaryPRKCAchr176458974964589769UHRF1BP1Lchr12100449860100449880
ovaryPRKCAchr176478450164784521chr4190179231190179251
pancreasPRKCAchr176435425764354277PRKCAchr176435670764356727
pancreasPRKCAchr176435477264354792DCAF7chr176162938861629408
pancreasPRKCAchr176435576264355782QRICH2chr177427574974275769
pancreasPRKCAchr176439021464390234chr177586307975863099
pancreasPRKCAchr176447784764477867chr174764052747640547
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 PRKCA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF854872PRKCA1140176457180864571947SLC45A31363101205633006205633180
M12996G6PD11671X153759627153763408PRKCA16642439176480606664806841
L13387PRKCA1682176441040764411088PAFAH1B168327491725703402586175
AK098118PRKCA12037176468263764684673LYZ20322662126974738369748013
BG998534PRKCA26267176432702564327270PBX12604001164712457164712597
CV427033PRKCA1236176469098464691219ATP2A222840512110759445110759622
BF665493PRKCA1387176451141164511798GALNT133683942154989282154989308
BF815383ALG54306133752409537539828PRKCA306486176452479864524978

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 # sample252 2 15 11   11 1
GAIN (# sample)242 2 12  1   11 1
LOSS (# sample)1     3 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=62)
Stat. for Synonymous SNVs
(# total SNVs=30)
Stat. for Deletions
(# total SNVs=2)
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
chr17:64738759-64738759p.V469I4
chr17:64785022-64785022p.E593E3
chr17:64637478-64637478p.P98P3
chr17:64783070-64783070p.E564G2
chr17:64683239-64683239p.N182fs*22
chr17:64492367-64492367p.S85F2
chr17:64685078-64685078p.L277L2
chr17:64641554-64641554p.G152R2
chr17:64737785-64737785p.A444V2
chr17:64685162-64685162p.F305F2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2 1132 3 2  1152  114 12
# mutation2 1112 3 2  1252  114 14
nonsynonymous SNV1 162 2    751  83 9
synonymous SNV1  5  1 2  5 1  31 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])

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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
chr17:64299066p.E33Q3
chr17:64637478p.P98P3
chr17:64728899p.D338N2
chr17:64637530p.G152R2
chr17:64734896p.F415F2
chr17:64641554p.D116N2
chr17:64685162p.F305F2
chr17:64683246p.L668L1
chr17:64782999p.A12A1
chr17:64299005p.C135C1

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 PRKCA 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 PRKCA

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

ACAN,ANKH,CHST3,DEFB127,ENPP6,FNDC3B,GLS,
IFNAR2,MAML2,MFGE8,NRP2,PGM5P2,PMP2,PRKCA,
PROS1,PTPN14,SLC23A2,SOX6,TIAM2,TRPV4,ZC3H12C
AKT3,ANP32E,ANTXR1,DPYSL3,GRIN2A,HDAC4,IL7,
KCNJ16,KCNJ2,KIAA1024,MOXD1,MUC16,OSMR,PRICKLE1,
PRKCA,PROS1,SCN3A,SOCS5,STAC,TLE4,TRPC1

ANKRD36BP1,APPBP2,ASH1L,BPTF,CLTC,CPD,DCAF7,
DYRK2,ERN1,HELZ,HIPK1,KIAA1211,LOC651250,MAGI1,
MED13,NCOA1,PHF12,PRKCA,RAPH1,SP1,USP32
AKAP6,BNC2,METTL24,DMD,DOCK3,CCSER2,ITPKB,
JMY,KCNB1,CTIF,MYH11,NBEA,NRXN3,TENM1,
TENM3___TENM1,PIP5K1C,PRICKLE2,PRKCA,SVIL,TLN1,TSPAN18
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 PRKCA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P17252; -.
ChemistryChEMBL CHEMBL2096620; -.
ChemistryGuidetoPHARMACOLOGY 1482; -.
Organism-specific databasesPharmGKB PA33759; -.
Organism-specific databasesCTD 5578; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00144protein kinase C, alphaapproved; nutraceuticalPhosphatidylserine
DB00163protein kinase C, alphaapproved; nutraceuticalVitamin E
DB00945protein kinase C, alphaapprovedAcetylsalicylic acid
DB00675protein kinase C, alphaapprovedTamoxifen
DB01115protein kinase C, alphaapprovedNifedipine
DB00877protein kinase C, alphaapproved; investigationalSirolimus
DB00864protein kinase C, alphaapproved; investigationalTacrolimus
DB00608protein kinase C, alphaapprovedChloroquine
DB00171protein kinase C, alphaapproved; nutraceuticalAdenosine triphosphate
DB00441protein kinase C, alphaapprovedGemcitabine
DB01001protein kinase C, alphaapprovedSalbutamol
DB00125protein kinase C, alphaapproved; nutraceuticalL-Arginine
DB00155protein kinase C, alphaapproved; nutraceuticalL-Citrulline
DB00435protein kinase C, alphaapprovedNitric Oxide


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Cross referenced IDs for PRKCA
* 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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