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 PRKAR2B
Basic gene info.Gene symbolPRKAR2B
Gene nameprotein kinase, cAMP-dependent, regulatory, type II, beta
SynonymsPRKAR2|RII-BETA
CytomapUCSC genome browser: 7q22
Genomic locationchr7 :106685177-106802256
Type of geneprotein-coding
RefGenesNM_002736.2,
Ensembl idENSG00000005249
DescriptionH_RG363E19.2WUGSC:H_RG363E19.2cAMP-dependent protein kinase type II-beta regulatory chaincAMP-dependent protein kinase type II-beta regulatory subunit
Modification date20141207
dbXrefs MIM : 176912
HGNC : HGNC
Ensembl : ENSG00000005249
HPRD : 01486
Vega : OTTHUMG00000137418
ProteinUniProt: P31323
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKAR2B
BioGPS: 5577
Gene Expression Atlas: ENSG00000005249
The Human Protein Atlas: ENSG00000005249
PathwayNCI Pathway Interaction Database: PRKAR2B
KEGG: PRKAR2B
REACTOME: PRKAR2B
ConsensusPathDB
Pathway Commons: PRKAR2B
MetabolismMetaCyc: PRKAR2B
HUMANCyc: PRKAR2B
RegulationEnsembl's Regulation: ENSG00000005249
miRBase: chr7 :106,685,177-106,802,256
TargetScan: NM_002736
cisRED: ENSG00000005249
ContextiHOP: PRKAR2B
cancer metabolism search in PubMed: PRKAR2B
UCL Cancer Institute: PRKAR2B
Assigned class in ccmGDBB - This gene belongs to cancer gene.

Top
Phenotypic Information for PRKAR2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKAR2B
Familial Cancer Database: PRKAR2B
* 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 176912; gene.
Orphanet
DiseaseKEGG Disease: PRKAR2B
MedGen: PRKAR2B (Human Medical Genetics with Condition)
ClinVar: PRKAR2B
PhenotypeMGI: PRKAR2B (International Mouse Phenotyping Consortium)
PhenomicDB: PRKAR2B

Mutations for PRKAR2B
* 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
liverPRKAR2Bchr7106795985106795985COG5chr7106894145106894145
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 PRKAR2B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
GW493216PRKAR2B181317106729510106729633RNF121117162117166418771664232
T06404UNC5D119483531712335317316PRKAR2B1943607106689677106689843

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 # sample 1      2    1   
GAIN (# sample) 1      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)

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=4

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=9)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr7:106685448-106685448p.A32A4
chr7:106786832-106786832p.E223*3
chr7:106791406-106791406p.A261S2
chr7:106791470-106791470p.?2
chr7:106797673-106797673p.R343*2
chr7:106786820-106786820p.G219W2
chr7:106685560-106685560p.P70S2
chr7:106797436-106797436p.S309L2
chr7:106710728-106710728p.P104A2
chr7:106797452-106797452p.F314F2

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
# sample11131 2 2  141  67 2
# mutation11131 2 2  141  68 2
nonsynonymous SNV11131 2 2   21  47 1
synonymous SNV           12   21 1
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
chr7:106786820p.G219R2
chr7:106786832p.D186D1
chr7:106797681p.S309L1
chr7:106781346p.G188G1
chr7:106786833p.F314F1
chr7:106797730p.D195V1
chr7:106781369p.E317Q1
chr7:106786905p.R196I1
chr7:106797745p.S345L1
chr7:106781375p.D206D1

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 PRKAR2B 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 PRKAR2B

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

AFF3,AHCYL2,CRBN,DMXL1,EPB41L5,HBP1,ICA1L,
KANSL3,MTMR10,NDFIP1,PCLO,PRKAR2B,PRLR,PTPLAD1,
RSBN1L,SALL2,TAF9B,TLK1,TMEM209,UBN2,WASL
ACO1,AOC3,FAM213A,PQLC2L,CD36,EBF1,FAM89A,
GYG2,HRASLS5,KCNIP2,MARC1,PCYOX1,PDE3B,PEX19,
PLIN1,PPARG,PPP2R5A,PRKAR2B,RTN3,SIK2,UBA2

ABCA6,ABCD2,ACSM5,ADH1B,ARHGEF6,SMCO3,CD300LG,
CD36,FABP4,GGTA1P,GNG2,HEPACAM,LOC339524,PDE1B,
PI16,PLIN4,PRKAR2B,RBP7,SEMA3G,SGCG,TUSC5
ANXA1,ARL13B,TMEM263,CCDC169,C2orf74,CDK2AP1,CTPS1,
FGF10,MFAP5,MTERF2,MYEF2,NFYB,PRKAR2B,PSMC3IP,
RAD51D,RGS16,RSPO2,SCML2,TPD52L1,WBP4,ZNHIT6
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 PRKAR2B
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P31323; -.
Organism-specific databasesPharmGKB PA33758; -.
Organism-specific databasesCTD 5577; -.

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, betaapproved; nutraceuticalL-Arginine
DB00155protein kinase, cAMP-dependent, regulatory, type II, betaapproved; nutraceuticalL-Citrulline
DB00435protein kinase, cAMP-dependent, regulatory, type II, betaapprovedNitric Oxide
DB00988protein kinase, cAMP-dependent, regulatory, type II, betaapprovedDopamine
DB00171protein kinase, cAMP-dependent, regulatory, type II, betaapproved; nutraceuticalAdenosine triphosphate
DB00770protein kinase, cAMP-dependent, regulatory, type II, betaapproved; investigationalAlprostadil
DB00668protein kinase, cAMP-dependent, regulatory, type II, betaapprovedEpinephrine
DB00131protein kinase, cAMP-dependent, regulatory, type II, betaapproved; nutraceuticalAdenosine monophosphate
DB00396protein kinase, cAMP-dependent, regulatory, type II, betaapprovedProgesterone


Top
Cross referenced IDs for PRKAR2B
* 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