Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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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 PRKACA
Basic gene info.Gene symbolPRKACA
Gene nameprotein kinase, cAMP-dependent, catalytic, alpha
SynonymsPKACA
CytomapUCSC genome browser: 19p13.1
Genomic locationchr19 :14202506-14228559
Type of geneprotein-coding
RefGenesNM_002730.3,
NM_207518.1,
Ensembl idENSG00000072062
DescriptionPKA C-alphacAMP-dependent protein kinase catalytic subunit alphaprotein kinase A catalytic subunit
Modification date20141207
dbXrefs MIM : 601639
HGNC : HGNC
Ensembl : ENSG00000072062
HPRD : 03382
Vega : OTTHUMG00000182051
ProteinUniProt: P17612
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PRKACA
BioGPS: 5566
Gene Expression Atlas: ENSG00000072062
The Human Protein Atlas: ENSG00000072062
PathwayNCI Pathway Interaction Database: PRKACA
KEGG: PRKACA
REACTOME: PRKACA
ConsensusPathDB
Pathway Commons: PRKACA
MetabolismMetaCyc: PRKACA
HUMANCyc: PRKACA
RegulationEnsembl's Regulation: ENSG00000072062
miRBase: chr19 :14,202,506-14,228,559
TargetScan: NM_002730
cisRED: ENSG00000072062
ContextiHOP: PRKACA
cancer metabolism search in PubMed: PRKACA
UCL Cancer Institute: PRKACA
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for PRKACA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PRKACA
Familial Cancer Database: PRKACA
* 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 601639; gene.
615830; phenotype.
Orphanet 401920; Fibrolamellar hepatocellular carcinoma.
DiseaseKEGG Disease: PRKACA
MedGen: PRKACA (Human Medical Genetics with Condition)
ClinVar: PRKACA
PhenotypeMGI: PRKACA (International Mouse Phenotyping Consortium)
PhenomicDB: PRKACA

Mutations for PRKACA
* 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
ovaryPRKACAchr191421932214219342PRKACAchr191422448714224507
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 PRKACA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DR006627PRKACA23456191421757214228556ENTPD1452694109762743997627682
BQ278860PRKACA1531191420331114203841NDOR15308989140110420140110940

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      
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)

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)		Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)		Stat. for Insertions
(# total SNVs=1)

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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
chr19:14208416-14208416p.L206R4
chr19:14213642-14213642p.E108Q3
chr19:14218165-14218165p.A35S2
chr19:14208444-14208444p.W197G2
chr19:14213716-14213716p.L83P2
chr19:14208277-14208277p.D221N2
chr19:14213652-14213652p.L104L2
chr19:14213659-14213659p.P102L2
chr19:14208394-14208394p.S213R1
chr19:14217673-14217673p.R46*1

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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
# sample 3 4  4 2  3 1 134 7
# mutation 3 3  4 2  3 1 134 8
nonsynonymous SNV 2 1  4 1  2 1 131 5
synonymous SNV 1 2    1  1     3 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
chr19:14208444p.A234T,PRKACA2
chr19:14213716p.L83P,PRKACA2
chr19:14208238p.C200C,PRKACA2
chr19:14208433p.W197R,PRKACA2
chr19:14213667p.D291E,PRKACA1
chr19:14204026p.F109L,PRKACA1
chr19:14213684p.I251I,PRKACA1
chr19:14204497p.L104L,PRKACA1
chr19:14208462p.P244L,PRKACA1
chr19:14208185p.L104F,PRKACA1

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 PRKACA 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 PRKACA

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

AP1M1,ASF1B,BRD4,C19orf44,C19orf53,CC2D1A,CHERP,
DCAF15,DDA1,DDX39A,FAM32A,LPHN1,MED26,NACC1,
PRKACA,RAB8A,RAD23A,RAVER1,TBX22,TECR,WIZ		ACAT1,ATG9A,ATP5G3,PRADC1,C6orf106,CDK16,CHCHD3,
HOXA10,HSPB2,HSPB6,IMMT,MAP4,OGDH,OPTN,
PDHB,PGM1,PRKACA,SGCG,ST3GAL3,SYNPO,TBX15

ABHD8,AP1M1,ATN1,DVL3,EHD2,EPS15L1,FAM127C,
MARCH2,MARK4,MLLT1,NFIX,PACS1,PALM2-AKAP2,PIP5K1C,
PRAF2,PRKACA,INAFM1,TCEAL6,TCF7L1,WIZ,ZNF358		ADD1,ARL8A,ATN1,BCL9L,C6orf106,CASZ1,CCDC92,
CDC42EP4,DAPK3,EHBP1L1,FXR2,GDI1,KCTD2,LRSAM1,
MAPK8IP2,MICALL1,PHF13,PRKACA,SEPT9,TUBB2A,TUBB4A
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 PRKACA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P17612; -.
ChemistryChEMBL CHEMBL2094138; -.
ChemistryGuidetoPHARMACOLOGY 1476; -.
Organism-specific databasesPharmGKB PA33748; -.
Organism-specific databasesCTD 5566; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB01919protein kinase, cAMP-dependent, catalytic, alphaexperimentalPentanal
DB01940protein kinase, cAMP-dependent, catalytic, alphaexperimentalBalanol Analog 2
DB02155protein kinase, cAMP-dependent, catalytic, alphaexperimentalBalanol Analog 8
DB02440protein kinase, cAMP-dependent, catalytic, alphaexperimentalN-Octane
DB02482protein kinase, cAMP-dependent, catalytic, alphaexperimentalPhosphonothreonine
DB02611protein kinase, cAMP-dependent, catalytic, alphaexperimentalBalanol Analog 1
DB03374protein kinase, cAMP-dependent, catalytic, alphaexperimental3,5-Diiodotyrosine
DB04098protein kinase, cAMP-dependent, catalytic, alphaexperimentalBalanol
DB04522protein kinase, cAMP-dependent, catalytic, alphaexperimentalPhosphonoserine
DB04530protein kinase, cAMP-dependent, catalytic, alphaexperimentalS,S-(2-Hydroxyethyl)Thiocysteine
DB04707protein kinase, cAMP-dependent, catalytic, alphaexperimentalHYDROXYFASUDIL
DB06959protein kinase, cAMP-dependent, catalytic, alphaexperimental(1S)-2-(1H-INDOL-3-YL)-1-{[(5-ISOQUINOLIN-6-YLPYRIDIN-3-YL)OXY]METHYL}ETHYLAMINE
DB06977protein kinase, cAMP-dependent, catalytic, alphaexperimental(2S)-1-{[5-(1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}-3-[(7AS)-7AH-INDOL-3-YL]PROPAN-2-AMINE
DB07107protein kinase, cAMP-dependent, catalytic, alphaexperimental(1S)-2-(1H-INDOL-3-YL)-1-[({5-[(E)-2-PYRIDIN-4-YLVINYL]PYRIDIN-3-YL}OXY)METHYL]ETHYLAMINE
DB07124protein kinase, cAMP-dependent, catalytic, alphaexperimental(2S)-1-(6H-INDOL-3-YL)-3-{[5-(7H-PYRAZOLO[3,4-C]PYRIDIN-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE
DB07204protein kinase, cAMP-dependent, catalytic, alphaexperimental(1S)-1-(1H-INDOL-3-YLMETHYL)-2-(2-PYRIDIN-4-YL-[1,7]NAPHTYRIDIN-5-YLOXY)-EHYLAMINE
DB07235protein kinase, cAMP-dependent, catalytic, alphaexperimentalN-[(1S)-2-AMINO-1-(2,4-DICHLOROBENZYL)ETHYL]-5-[2-(METHYLAMINO)PYRIMIDIN-4-YL]THIOPHENE-2-CARBOXAMIDE
DB07458protein kinase, cAMP-dependent, catalytic, alphaexperimental3-(1H-INDOL-3-YL)-4-{1-[2-(1-METHYLPYRROLIDIN-2-YL)ETHYL]-1H-INDOL-3-YL}-1H-PYRROLE-2,5-DIONE
DB07583protein kinase, cAMP-dependent, catalytic, alphaexperimental(4R,2S)-5'-(4-(4-CHLOROBENZYLOXY)PYRROLIDIN-2-YLMETHANESULFONYL)ISOQUINOLINE
DB07854protein kinase, cAMP-dependent, catalytic, alphaexperimentalN-METHYL-1-[4-(9H-PURIN-6-YL)PHENYL]METHANAMINE
DB07855protein kinase, cAMP-dependent, catalytic, alphaexperimental(S)-1-PHENYL-1-[4-(9H-PURIN-6-YL)PHENYL]METHANAMINE
DB07856protein kinase, cAMP-dependent, catalytic, alphaexperimental6-{4-[4-(4-CHLOROPHENYL)PIPERIDIN-4-YL]PHENYL}-9H-PURINE
DB07857protein kinase, cAMP-dependent, catalytic, alphaexperimental(2R)-2-(4-CHLOROPHENYL)-2-[4-(1H-PYRAZOL-4-YL)PHENYL]ETHANAMINE
DB07858protein kinase, cAMP-dependent, catalytic, alphaexperimental(2S)-2-(4-CHLOROPHENYL)-2-[4-(1H-PYRAZOL-4-YL)PHENYL]ETHANAMINE
DB07859protein kinase, cAMP-dependent, catalytic, alphaexperimental4-(4-CHLOROPHENYL)-4-[4-(1H-PYRAZOL-4-YL)PHENYL]PIPERIDINE
DB07860protein kinase, cAMP-dependent, catalytic, alphaexperimental(2R)-2-(4-CHLOROPHENYL)-2-PHENYLETHANAMINE
DB07876protein kinase, cAMP-dependent, catalytic, alphaexperimental(S)-2-METHYL-1-[(4-METHYL-5-ISOQUINOLINE)SULFONYL]-HOMOPIPERAZINE
DB07947protein kinase, cAMP-dependent, catalytic, alphaexperimentalISOQUINOLINE-5-SULFONIC ACID (2-(2-(4-CHLOROBENZYLOXY)ETHYLAMINO)ETHYL)AMIDE
DB07995protein kinase, cAMP-dependent, catalytic, alphaexperimentalN-[2-(4-BROMOCINNAMYLAMINO)ETHYL]-5-ISOQUINOLINE SULFONAMIDE
DB07996protein kinase, cAMP-dependent, catalytic, alphaexperimental1-(5-ISOQUINOLINESULFONYL)-2-METHYLPIPERAZINE
DB07997protein kinase, cAMP-dependent, catalytic, alphaexperimentalN-[2-(METHYLAMINO)ETHYL]-5-ISOQUINOLINESULFONAMIDE
DB08070protein kinase, cAMP-dependent, catalytic, alphaexperimental2-[4-(3-METHYL-1H-PYRAZOL-4-YL)PHENYL]ETHANAMINE
DB08073protein kinase, cAMP-dependent, catalytic, alphaexperimental(2S)-1-(1H-INDOL-3-YL)-3-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}PROPAN-2-AMINE
DB08113protein kinase, cAMP-dependent, catalytic, alphaexperimental3-pyridin-4-yl-1H-indazole
DB08114protein kinase, cAMP-dependent, catalytic, alphaexperimental5-benzyl-1,3-thiazol-2-amine
DB08148protein kinase, cAMP-dependent, catalytic, alphaexperimental1-[4-(4-chlorophenyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine
DB08149protein kinase, cAMP-dependent, catalytic, alphaexperimental1-[4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-yl]methanamine
DB08150protein kinase, cAMP-dependent, catalytic, alphaexperimental4-(4-chlorobenzyl)-1-(7H-pyrrolo[2,3-d]pyrimidin-4-yl)piperidin-4-aminium
DB08162protein kinase, cAMP-dependent, catalytic, alphaexperimental5-(1,4-DIAZEPAN-1-SULFONYL)ISOQUINOLINE
DB08231protein kinase, cAMP-dependent, catalytic, alphaexperimentalMYRISTIC ACID
DB08568protein kinase, cAMP-dependent, catalytic, alphaexperimental(2S)-1-{[5-(3-METHYL-1H-INDAZOL-5-YL)PYRIDIN-3-YL]OXY}-3-PHENYLPROPAN-2-AMINE
DB08569protein kinase, cAMP-dependent, catalytic, alphaexperimental3-PYRIDIN-4-YL-2,4-DIHYDRO-INDENO[1,2-.C.] PYRAZOLE
DB08756protein kinase, cAMP-dependent, catalytic, alphaexperimental(R)-TRANS-4-(1-AMINOETHYL)-N-(4-PYRIDYL) CYCLOHEXANECARBOXAMIDE
DB00938protein kinase, cAMP-dependent, catalytic, alphaapprovedSalmeterol
DB00125protein kinase, cAMP-dependent, catalytic, alphaapproved; nutraceuticalL-Arginine
DB00435protein kinase, cAMP-dependent, catalytic, alphaapprovedNitric Oxide
DB00864protein kinase, cAMP-dependent, catalytic, alphaapproved; investigationalTacrolimus


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Cross referenced IDs for PRKACA
* 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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