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 PRKAB2
Basic gene info.Gene symbolPRKAB2
Gene nameprotein kinase, AMP-activated, beta 2 non-catalytic subunit
Synonyms-
CytomapUCSC genome browser: 1q21.1
Genomic locationchr1 :146626684-146644129
Type of geneprotein-coding
RefGenesNM_005399.4,
NR_103870.1,NR_103871.1,
Ensembl idENSG00000266198
Description5'-AMP-activated protein kinase subunit beta-25'-AMP-activated protein kinase, beta-2 subunitAMP-activated protein kinase beta 2 non-catalytic subunitAMPK beta 2AMPK beta-2 chainAMPK subunit beta-2
Modification date20141207
dbXrefs MIM : 602741
HGNC : HGNC
Ensembl : ENSG00000131791
HPRD : 04117
Vega : OTTHUMG00000014032
ProteinUniProt: O43741
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKAB2
BioGPS: 5565
Gene Expression Atlas: ENSG00000266198
The Human Protein Atlas: ENSG00000266198
PathwayNCI Pathway Interaction Database: PRKAB2
KEGG: PRKAB2
REACTOME: PRKAB2
ConsensusPathDB
Pathway Commons: PRKAB2
MetabolismMetaCyc: PRKAB2
HUMANCyc: PRKAB2
RegulationEnsembl's Regulation: ENSG00000266198
miRBase: chr1 :146,626,684-146,644,129
TargetScan: NM_005399
cisRED: ENSG00000266198
ContextiHOP: PRKAB2
cancer metabolism search in PubMed: PRKAB2
UCL Cancer Institute: PRKAB2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PRKAB2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKAB2
Familial Cancer Database: PRKAB2
* 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

check002.gifOthers
OMIM 602741; gene.
Orphanet
DiseaseKEGG Disease: PRKAB2
MedGen: PRKAB2 (Human Medical Genetics with Condition)
ClinVar: PRKAB2
PhenotypeMGI: PRKAB2 (International Mouse Phenotyping Consortium)
PhenomicDB: PRKAB2

Mutations for PRKAB2
* 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
ovaryPRKAB2chr1146640224146640244LOC100289211chr1146947738146947758
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 PRKAB2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA824273PRKAB214881146638424146644053RFWD24865561176118142176118212
DA947002RAB5A118631998858919988773PRKAB21872911146628365146628469
AA836812ANO61381124582574945826129PRKAB23824431146626712146626773
BX482434PRKAB29681146636898146636957ERG63584213976875339769274

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 # sample      1 2        
GAIN (# sample)        2        
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
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
chr1:146638439-146638439p.H135Y2
chr1:146639438-146639438p.R77R2
chr1:146634107-146634107p.A195V2
chr1:146639461-146639461p.V70I2
chr1:146633313-146633313p.H240L2
chr1:146638126-146638126p.F163F2
chr1:146639413-146639413p.G86R2
chr1:146634073-146634073p.P206P1
chr1:146638429-146638429p.S138*1
chr1:146631154-146631154p.K270M1

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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
# sample11 5       311  32 2
# mutation21 5       311  42 2
nonsynonymous SNV1  4       111  21 1
synonymous SNV11 1       2    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])

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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
chr1:146639438p.R77R2
chr1:146638499p.I115V1
chr1:146631209p.P104S1
chr1:146639359p.V90A1
chr1:146633349p.G87G1
chr1:146639400p.R82H1
chr1:146634020p.P78H1
chr1:146639408p.V252F1
chr1:146634073p.A228V1
chr1:146639424p.R77R1

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 PRKAB2 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 PRKAB2

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

ABL2,ARL10,ARNT,BCL9,DIEXF,CEP350,CHD1L,
GATAD2B,KCTD20,LOC200030,MTR,NBPF10,PIP5K1A,POGZ,
PPFIBP1,PRKAB2,RASAL2,RNF115,RPRD2,ZKSCAN8,ZNF391
AGL,ASB14,ASB8,BVES,CAP2,DCAF6,KIF1B,
MEF2C,PAIP2B,PHTF2,PPP2R3A,PRKAA2,PRKAB2,SYNPO2,
TMEM182,TMEM38B,UBR3,USP13,XPO4,ZNF106,ZYG11B

ARID4B,ARNT,ASH1L,ATF6,SWT1,CREBRF,CAMSAP2,
CEP350,DISP1,GLDN,KCTD7,KLHL20,NEK7,OTUD7B,
PRKAB2,RCOR3,SLC12A6,SOCS5,TOR1AIP1,TSHZ2,YY1AP1
ASPN,C14orf132,C3orf18,METTL24,CAMK2G,CASQ1,DES,
HAND1,ILK,KCTD8,MBNL2,MYL9,PDLIM3,PDZRN4,
PIPOX,PNCK,PPP1R1A,PRKAB2,TPM1,TPM2,VEZF1
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 PRKAB2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL3038453; -.
Organism-specific databasesPharmGKB PA33747; -.
Organism-specific databasesCTD 5565; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00131protein kinase, AMP-activated, beta 2 non-catalytic subunitapproved; nutraceuticalAdenosine monophosphate
DB00171protein kinase, AMP-activated, beta 2 non-catalytic subunitapproved; nutraceuticalAdenosine triphosphate
DB00412protein kinase, AMP-activated, beta 2 non-catalytic subunitapproved; investigationalRosiglitazone
DB01132protein kinase, AMP-activated, beta 2 non-catalytic subunitapproved; investigationalPioglitazone
DB00331protein kinase, AMP-activated, beta 2 non-catalytic subunitapprovedMetformin


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Cross referenced IDs for PRKAB2
* 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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