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 PRKAR2A
Basic gene info.Gene symbolPRKAR2A
Gene nameprotein kinase, cAMP-dependent, regulatory, type II, alpha
SynonymsPKR2|PRKAR2
CytomapUCSC genome browser: 3p21.3-p21.2
Genomic locationchr3 :48788092-48885270
Type of geneprotein-coding
RefGenesNM_004157.2,
Ensembl idENSG00000114302
DescriptioncAMP-dependent protein kinase regulatory subunit RII alphacAMP-dependent protein kinase type II-alpha regulatory subunitprotein kinase A, RII-alpha subunit
Modification date20141207
dbXrefs MIM : 176910
HGNC : HGNC
Ensembl : ENSG00000114302
HPRD : 01484
Vega : OTTHUMG00000133540
ProteinUniProt: P13861
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKAR2A
BioGPS: 5576
Gene Expression Atlas: ENSG00000114302
The Human Protein Atlas: ENSG00000114302
PathwayNCI Pathway Interaction Database: PRKAR2A
KEGG: PRKAR2A
REACTOME: PRKAR2A
ConsensusPathDB
Pathway Commons: PRKAR2A
MetabolismMetaCyc: PRKAR2A
HUMANCyc: PRKAR2A
RegulationEnsembl's Regulation: ENSG00000114302
miRBase: chr3 :48,788,092-48,885,270
TargetScan: NM_004157
cisRED: ENSG00000114302
ContextiHOP: PRKAR2A
cancer metabolism search in PubMed: PRKAR2A
UCL Cancer Institute: PRKAR2A
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PRKAR2A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKAR2A
Familial Cancer Database: PRKAR2A
* 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_INTEGRATION_OF_ENERGY_METABOLISM

check002.gifOthers
OMIM 176910; gene.
Orphanet
DiseaseKEGG Disease: PRKAR2A
MedGen: PRKAR2A (Human Medical Genetics with Condition)
ClinVar: PRKAR2A
PhenotypeMGI: PRKAR2A (International Mouse Phenotyping Consortium)
PhenomicDB: PRKAR2A

Mutations for PRKAR2A
* 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
ovaryPRKAR2Achr34879805248798072chr34859705648597076
pancreasPRKAR2Achr34883194248831962chr34876016148760181
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 PRKAR2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK299521CTU21664168877291188779212PRKAR2A656117234878560548786121
BG990796PRKAR2A2123434878825748788469MRPS522832229578095895781052

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
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
chr3:48793865-48793865p.D296N3
chr3:48810487-48810487p.Q199Q2
chr3:48789613-48789613p.C359*1
chr3:48831472-48831472p.E103E1
chr3:48793818-48793818p.R311S1
chr3:48810497-48810497p.S196Y1
chr3:48845102-48845102p.R93I1
chr3:48789616-48789616p.K358N1
chr3:48793838-48793838p.E305*1
chr3:48810499-48810499p.R195R1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 5  1    2 1  1317
# mutation21 5  1    2 1  1317
nonsynonymous SNV21 4       2 1  1114
synonymous SNV   1  1          2 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
chr3:48789132p.K358N1
chr3:48820420p.S80L1
chr3:48789616p.K358E1
chr3:48820505p.A72T1
chr3:48789618p.R329R1
chr3:48820513p.R23Q1
chr3:48789703p.F298V1
chr3:48828006p.I281I1
chr3:48793859p.S268L1
chr3:48831472p.S196Y1

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 PRKAR2A 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 PRKAR2A

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

APPL1,ASXL2,BIRC6,CCNT1,CLOCK,DDI2,DPP8,
EXOC6B,GTF2A1,PAFAH1B2,PBRM1,PPP4R2,PRKAR2A,RAD54L2,
REST,SETD2,SON,STRN,UHMK1,VPRBP,ZNF106
AHCYL2,APOOL,ATE1,CUL4A,DMD,DPP8,HBS1L,
HECTD1,HERC1,VWA8,KIF13A,LOC729082,LYRM7,MLXIP,
PPTC7,PRKAR2A,PYGO1,UBE3C,UBR3,USO1,ZYG11B

ANAPC1,ASXL2,ATE1,DDI2,LATS1,LMBRD2,MAN2A1,
NEU3,PDP2,PPP4R2,PRKAR2A,PTPLB,RAD54L2,RAPGEF6,
RC3H2,REST,ROCK2,RSC1A1,SERINC5,STRN,TGFBRAP1
AQR,AVL9,C9orf129,DNAJA4,EYA3,FAM199X,FMN1,
LMBRD2,MBNL3,MTMR8,NDUFS1,NHLRC2,PRKAR2A,PTPLB,
SBNO1,SMC5,STRN,TMEM184C,UHMK1,UNC13B,ZDHHC20
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 PRKAR2A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33757; -.
Organism-specific databasesCTD 5576; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125protein kinase, cAMP-dependent, regulatory, type II, alphaapproved; nutraceuticalL-Arginine
DB00155protein kinase, cAMP-dependent, regulatory, type II, alphaapproved; nutraceuticalL-Citrulline
DB00435protein kinase, cAMP-dependent, regulatory, type II, alphaapprovedNitric Oxide
DB00988protein kinase, cAMP-dependent, regulatory, type II, alphaapprovedDopamine
DB00171protein kinase, cAMP-dependent, regulatory, type II, alphaapproved; nutraceuticalAdenosine triphosphate
DB00770protein kinase, cAMP-dependent, regulatory, type II, alphaapproved; investigationalAlprostadil
DB00668protein kinase, cAMP-dependent, regulatory, type II, alphaapprovedEpinephrine
DB00131protein kinase, cAMP-dependent, regulatory, type II, alphaapproved; nutraceuticalAdenosine monophosphate
DB00396protein kinase, cAMP-dependent, regulatory, type II, alphaapprovedProgesterone


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Cross referenced IDs for PRKAR2A
* 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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