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 PRKACB
Basic gene info.Gene symbolPRKACB
Gene nameprotein kinase, cAMP-dependent, catalytic, beta
SynonymsPKA C-beta|PKACB
CytomapUCSC genome browser: 1p31.1
Genomic locationchr1 :84543744-84670979
Type of geneprotein-coding
RefGenesNM_001242857.2,
NM_001242858.2,NM_001242859.2,NM_001242860.2,NM_001242861.2,
NM_001242862.2,NM_001300915.1,NM_001300916.1,NM_001300917.1,
NM_002731.3,NM_182948.3,NM_207578.2,
Ensembl idENSG00000142875
DescriptioncAMP-dependent protein kinase catalytic beta subunit isoform 4abcAMP-dependent protein kinase catalytic subunit betaprotein kinase A catalytic subunit beta
Modification date20141207
dbXrefs MIM : 176892
HGNC : HGNC
Ensembl : ENSG00000142875
HPRD : 01482
Vega : OTTHUMG00000009975
ProteinUniProt: P22694
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKACB
BioGPS: 5567
Gene Expression Atlas: ENSG00000142875
The Human Protein Atlas: ENSG00000142875
PathwayNCI Pathway Interaction Database: PRKACB
KEGG: PRKACB
REACTOME: PRKACB
ConsensusPathDB
Pathway Commons: PRKACB
MetabolismMetaCyc: PRKACB
HUMANCyc: PRKACB
RegulationEnsembl's Regulation: ENSG00000142875
miRBase: chr1 :84,543,744-84,670,979
TargetScan: NM_001242857
cisRED: ENSG00000142875
ContextiHOP: PRKACB
cancer metabolism search in PubMed: PRKACB
UCL Cancer Institute: PRKACB
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRKACB in cancer cell metabolism1. Chen Y, Gao Y, Tian Y, Tian DL (2013) PRKACB is downregulated in non‑small cell lung cancer and exogenous PRKACB inhibits proliferation and invasion of LTEP‑A2 cells. Oncology letters 5: 1803-1808. go to article

Top
Phenotypic Information for PRKACB(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKACB
Familial Cancer Database: PRKACB
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 176892; gene.
176892; gene.
Orphanet
DiseaseKEGG Disease: PRKACB
MedGen: PRKACB (Human Medical Genetics with Condition)
ClinVar: PRKACB
PhenotypeMGI: PRKACB (International Mouse Phenotyping Consortium)
PhenomicDB: PRKACB

Mutations for PRKACB
* 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
ovaryPRKACBchr18455570384555723PRKACBchr18456547384565493
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 PRKACB related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA775505NEUROD6114073138020731380346PRKACB13955418464485884662339
BF944829PRKACB5827018463305784633274RYR3260452153402115334023790
DA223586SLC25A4413871156163908156169881PRKACB38652718463037884630519

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

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=5

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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
chr1:84663454-84663454p.W197R3
chr1:84679969-84679969p.T300M2
chr1:84649719-84649719p.?2
chr1:84649767-84649767p.I95M2
chr1:84644908-84644908p.E32G2
chr1:84649790-84649790p.F103S2
chr1:84662305-84662305p.P142P2
chr1:84700929-84700929p.E333Q2
chr1:84668371-84668371p.Y216*2
chr1:84647960-84647960p.K62K2

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
# sample1  5  2 3  731  33 4
# mutation1  4  2 3  831  33 4
nonsynonymous SNV1  3  2 3  631  32 2
synonymous SNV   1       2     1 2
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
chr1:84644908p.L215L,PRKACB2
chr1:84700929p.I216M,PRKACB2
chr1:84668407p.E20G,PRKACB2
chr1:84668410p.E320Q,PRKACB2
chr1:84650800p.K8N,PRKACB1
chr1:84668432p.W184C,PRKACB1
chr1:84544032p.G10V,PRKACB1
chr1:84650820p.H33Q1
chr1:84668433p.S21Y,PRKACB1
chr1:84544037p.M219I,PRKACB1

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 PRKACB 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 PRKACB

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

CDHR3,CPB1,DACH1,DCLK1,DNASE2B,FAM107B,FTO,
GPRIN3,GRIK1,IQSEC2,MACROD2,MAST4,PPP2R1B,PRKACB,
SAMD13,SEMA6D,SESN3,SIAH3,SMOC2,TSPAN1,UCN3
ACTR2,ADD3,AP3M1,ATP6V1A,CPD,CTBS,ERGIC2,
ERO1L,FBXW2,HFE,ITGAV,NIPA1,PRKACB,RPE,
SACM1L,SEC24A,SLC2A13,SLC41A2,SLC5A3,TMEM167A,ZNF518B

ABCD3,BCAS1,ENTPD5,EPB41L4B,FAM134B,FMO5,FPGT,
GNG12,LRRC19,MAGI3,PDCD4,PRKACB,SAMD13,SOS2,
SULT1B1,TMEM56,TRAK2,UGP2,USP53,ZNF774,ZNRF2
ACOT13,SMIM14,FXYD3,GOLPH3L,IFT74,MAL2,METAP1,
PCTP,PRKACB,SAMD13,SH3BGRL2,SLC35A3,SLC44A1,SNX7,
SPTLC1,TMEM87A,VAV3,XK,ZNF124,ZNF681,ZNF845
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 PRKACB
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P22694; -.
ChemistryChEMBL CHEMBL2918; -.
ChemistryGuidetoPHARMACOLOGY 1477; -.
ChemistryBindingDB P22694; -.
ChemistryChEMBL CHEMBL2918; -.
ChemistryGuidetoPHARMACOLOGY 1477; -.
Organism-specific databasesPharmGKB PA33749; -.
Organism-specific databasesPharmGKB PA33749; -.
Organism-specific databasesCTD 5567; -.
Organism-specific databasesCTD 5567; -.

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, catalytic, betaapproved; nutraceuticalL-Arginine
DB00155protein kinase, cAMP-dependent, catalytic, betaapproved; nutraceuticalL-Citrulline
DB00435protein kinase, cAMP-dependent, catalytic, betaapprovedNitric Oxide
DB00988protein kinase, cAMP-dependent, catalytic, betaapprovedDopamine
DB00171protein kinase, cAMP-dependent, catalytic, betaapproved; nutraceuticalAdenosine triphosphate
DB00770protein kinase, cAMP-dependent, catalytic, betaapproved; investigationalAlprostadil
DB00668protein kinase, cAMP-dependent, catalytic, betaapprovedEpinephrine
DB00131protein kinase, cAMP-dependent, catalytic, betaapproved; nutraceuticalAdenosine monophosphate
DB00396protein kinase, cAMP-dependent, catalytic, betaapprovedProgesterone
DB00938protein kinase, cAMP-dependent, catalytic, betaapprovedSalmeterol


Top
Cross referenced IDs for PRKACB
* 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