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 PRKAA1
Basic gene info.Gene symbolPRKAA1
Gene nameprotein kinase, AMP-activated, alpha 1 catalytic subunit
SynonymsAMPK|AMPKa1
CytomapUCSC genome browser: 5p12
Genomic locationchr5 :40759480-40798297
Type of geneprotein-coding
RefGenesNM_006251.5,
NM_206907.3,
Ensembl idENSG00000132356
Description5'-AMP-activated protein kinase catalytic subunit alpha-15'-AMP-activated protein kinase, catalytic alpha-1 chainACACA kinaseAMP -activate kinase alpha 1 subunitAMP-activated protein kinase, catalytic, alpha-1AMPK alpha 1AMPK subunit alpha-1HMGCR k
Modification date20141222
dbXrefs MIM : 602739
HGNC : HGNC
Ensembl : ENSG00000132356
HPRD : 04115
Vega : OTTHUMG00000162269
ProteinUniProt: Q13131
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKAA1
BioGPS: 5562
Gene Expression Atlas: ENSG00000132356
The Human Protein Atlas: ENSG00000132356
PathwayNCI Pathway Interaction Database: PRKAA1
KEGG: PRKAA1
REACTOME: PRKAA1
ConsensusPathDB
Pathway Commons: PRKAA1
MetabolismMetaCyc: PRKAA1
HUMANCyc: PRKAA1
RegulationEnsembl's Regulation: ENSG00000132356
miRBase: chr5 :40,759,480-40,798,297
TargetScan: NM_006251
cisRED: ENSG00000132356
ContextiHOP: PRKAA1
cancer metabolism search in PubMed: PRKAA1
UCL Cancer Institute: PRKAA1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRKAA1 in cancer cell metabolism1. Lee SJ, Kang BW, Chae YS, Kim HJ, Park SY, et al. (2014) Genetic Variations in STK11, PRKAA1, and TSC1 Associated with Prognosis for Patients with Colorectal Cancer. Annals of surgical oncology 21: 634-639. go to article

Top
Phenotypic Information for PRKAA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKAA1
Familial Cancer Database: PRKAA1
* 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
Nat Rev Drug Discovery, 2013, 12: 829, doi: 10.1038/nrd4145

check002.gifOthers
OMIM 602739; gene.
Orphanet
DiseaseKEGG Disease: PRKAA1
MedGen: PRKAA1 (Human Medical Genetics with Condition)
ClinVar: PRKAA1
PhenotypeMGI: PRKAA1 (International Mouse Phenotyping Consortium)
PhenomicDB: PRKAA1

Mutations for PRKAA1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 PRKAA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA340341IFT8116812110641691110641758PRKAA16358554076759940775608
BQ347750BAZ2B113062160268974160284931PRKAA130038854077697640777065
BE002414C5orf1519715133292049133292101PRKAA15821454076095440761110

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        
GAIN (# sample)        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=3

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr5:40767653-40767653p.Q246E2
chr5:40765100-40765100p.A354A2
chr5:40767729-40767729p.C220C2
chr5:40798245-40798245p.Q16R2
chr5:40775601-40775601p.Q92*2
chr5:40762927-40762927p.E545*2
chr5:40763048-40763048p.Q504Q2
chr5:40763109-40763109p.A484D1
chr5:40777689-40777689p.?1
chr5:40765006-40765006p.R386C1

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
# sample 4 10  4 1  7    15 7
# mutation 4 10  5 1  7    15 8
nonsynonymous SNV 1 8  2    6     4 6
synonymous SNV 3 2  3 1  1    11 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
chr5:40765109p.R386C,PRKAA12
chr5:40765006p.F351L,PRKAA12
chr5:40771830p.Q16R,PRKAA11
chr5:40763122p.S413T,PRKAA11
chr5:40798216p.G221G,PRKAA11
chr5:40771909p.R2H,PRKAA11
chr5:40764627p.P394A,PRKAA11
chr5:40798229p.A167T,PRKAA11
chr5:40765114p.R386H,PRKAA11
chr5:40775031p.Y140Y,PRKAA11

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 PRKAA1 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 PRKAA1

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.
Top
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))
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

BACH1,BMPR2,CAB39,CCNYL1,CREB1,GALNT3,ITGAV,
KIAA1033,KLHL2,LIMS1,MYCBP2,PRKAA1,RANBP2,RNF11,
SLC30A7,SLC41A2,SNTB2,SWAP70,TTC33,UTRN,YAP1
ACAP2,C16orf52,C5orf24,CHIC1,FAM91A1,FCHO2,FMR1,
FPGT,G2E3,LYSMD3,MIER1,MIER3,MTMR6,PRKAA1,
RASA1,SOCS4,STAM2,TMED7,TMEM30A,TROVE2,ZNF800

ABI1,C5orf24,C5orf51,CASC4,DCUN1D1,DNAJB14,FCHO2,
FGD4,GOLPH3,LMBRD2,LYSMD3,PAIP1,PLEKHA1,PRKAA1,
SLC35A3,TBC1D23,TMED7,TMF1,TTC33,ZFR,ZNF654
ARFIP1,SMIM15,C6orf211,CAAP1,CD46,FAM91A1,FCHO2,
GMFB,LYSMD3,PPIL4,PRKAA1,SACM1L,SIKE1,SLC30A9,
STAM2,STXBP3,TMED7,TMEM167A,TMEM68,TMX1,USP45
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 PRKAA1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB Q13131; -.
ChemistryChEMBL CHEMBL3038452; -.
ChemistryGuidetoPHARMACOLOGY 1541; -.
Organism-specific databasesPharmGKB PA33744; -.
Organism-specific databasesCTD 5562; -.

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, alpha 1 catalytic subunitapproved; nutraceuticalAdenosine monophosphate
DB00171protein kinase, AMP-activated, alpha 1 catalytic subunitapproved; nutraceuticalAdenosine triphosphate
DB00914protein kinase, AMP-activated, alpha 1 catalytic subunitapproved; withdrawnPhenformin
DB01174protein kinase, AMP-activated, alpha 1 catalytic subunitapprovedPhenobarbital
DB00412protein kinase, AMP-activated, alpha 1 catalytic subunitapproved; investigationalRosiglitazone
DB01132protein kinase, AMP-activated, alpha 1 catalytic subunitapproved; investigationalPioglitazone
DB00331protein kinase, AMP-activated, alpha 1 catalytic subunitapprovedMetformin


Top
Cross referenced IDs for PRKAA1
* 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