Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 PRKACG

Basic gene info.	Gene symbol	PRKACG
	Gene name	protein kinase, cAMP-dependent, catalytic, gamma
	Synonyms	KAPG\|PKACg
	Cytomap	UCSC genome browser: 9q13
	Genomic location	chr9 :71627448-71629039
	Type of gene	protein-coding
	RefGenes	NM_002732.3,
	Ensembl id	ENSG00000165059
	Description	PKA C-gammacAMP-dependent protein kinase catalytic subunit gammaserine(threonine) protein kinase
	Modification date	20141207
dbXrefs	MIM : 176893
	HGNC : HGNC
	Ensembl : ENSG00000165059
	HPRD : 01483
	Vega : OTTHUMG00000019974
Protein	UniProt: P22612 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKACG
	BioGPS: 5568
	Gene Expression Atlas: ENSG00000165059
	The Human Protein Atlas: ENSG00000165059
Pathway	NCI Pathway Interaction Database: PRKACG
	KEGG: PRKACG
	REACTOME: PRKACG
	ConsensusPathDB
	Pathway Commons: PRKACG
Metabolism	MetaCyc: PRKACG
	HUMANCyc: PRKACG
Regulation	Ensembl's Regulation: ENSG00000165059
	miRBase: chr9 :71,627,448-71,629,039
	TargetScan: NM_002732
	cisRED: ENSG00000165059
Context	iHOP: PRKACG
	cancer metabolism search in PubMed: PRKACG
	UCL Cancer Institute: PRKACG
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PRKACG(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRKACG
	Familial Cancer Database: PRKACG

* 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	176893; gene.
Orphanet
Disease	KEGG Disease: PRKACG
	MedGen: PRKACG (Human Medical Genetics with Condition)
	ClinVar: PRKACG
Phenotype	MGI: PRKACG (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKACG

Mutations for PRKACG

* 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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PRKACG related fusion information.

Head Gene

Tail Gene

Accession

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Gene_a

qStart_a

qEnd_a

Chromosome_a

tStart_a

tEnd_a

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

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SNV 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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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=48)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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Top 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 position	Mutation(aa)	Unique sampleID count
chr9:71628115-71628115	p.F298F	4
chr9:71628097-71628097	p.I304I	3
chr9:71628435-71628435	p.V192M	3
chr9:71628114-71628114	p.A299T	3
chr9:71628877-71628877	p.F44F	3
chr9:71628152-71628152	p.R286K	3
chr9:71628289-71628289	p.Y240Y	2
chr9:71628484-71628484	p.I175I	2
chr9:71628589-71628589	p.S140R	2
chr9:71628409-71628409	p.C200C	2

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	3		11			3		2			2	1	1		1	17	7		12
# mutation	1	3		10			3		2			2	1	1		1	19	8		12
nonsynonymous SNV		1		6			1		2			2	1	1			8	5		8
synonymous SNV	1	2		4			2									1	11	3		4

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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr9:71628877	p.F44F	3
chr9:71628097	p.I304I	3
chr9:71628114	p.C200C	2
chr9:71628484	p.A299T	2
chr9:71628130	p.K293K	2
chr9:71628979	p.V192M	2
chr9:71628021	p.I175I	2
chr9:71628409	p.R48K	2
chr9:71628435	p.D330N	2
chr9:71628059	p.P317L	2

Other 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

Copy Number for PRKACG 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 PRKACG

Gene 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.

Differential 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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CNV 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

Co-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


CLRN2,KRTAP19-2,KRTAP25-1,KRTAP6-1,MUC17,OPRM1,OR11A1, OR13F1,OR4C16,OR4L1,OR5AP2,OR5D18,OR5L2,OR6C65, OR6C75,OR8H3,POM121L12,PRKACG,REG1P,TAAR2,TAAR5	SLC35G3,AMZ2P1,CCDC70,CSNK1A1P1,DPPA2,ELMOD1,GLT6D1, KRTAP9-4,LILRP2,OR10G3,OR2T2,OR4A5,OR5F1,OR7G3, OR8H2,PRB1,PRKACG,RAB9BP1,SNORA32,SNORA71C,SVOP

BMPER,NAT16,CCDC144NL,CTAG1B,CTXN3,DYNLL2,KCNIP4, KRTAP10-10,KRTAP10-5,LOC389493,LOC572558,OR51B4,OR52D1,POTEH, PRKACG,SLC10A4,SLC6A11,TMEM213,UBE2U,WDR87,ZNF492	SLC35G3,BEND2,LINC00305,SSMEM1,CD300LD,FAM74A4,GAGE10, LRIT1,MSX2P1,NXF4,OR52E6,PAPOLB,PLCZ1,PRKACG, SCARNA16,SLC22A24,SLC9C2,SPRR2G,STRA8,TRIM24,UBASH3B, ZN

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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 PRKACG

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL2094138; -.
Chemistry	GuidetoPHARMACOLOGY	1478; -.
Organism-specific databases	PharmGKB	PA33750; -.
Organism-specific databases	CTD	5568; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00125	protein kinase, cAMP-dependent, catalytic, gamma	approved; nutraceutical	L-Arginine
DB00155	protein kinase, cAMP-dependent, catalytic, gamma	approved; nutraceutical	L-Citrulline
DB00435	protein kinase, cAMP-dependent, catalytic, gamma	approved	Nitric Oxide
DB00988	protein kinase, cAMP-dependent, catalytic, gamma	approved	Dopamine
DB00171	protein kinase, cAMP-dependent, catalytic, gamma	approved; nutraceutical	Adenosine triphosphate
DB00770	protein kinase, cAMP-dependent, catalytic, gamma	approved; investigational	Alprostadil
DB00668	protein kinase, cAMP-dependent, catalytic, gamma	approved	Epinephrine
DB00131	protein kinase, cAMP-dependent, catalytic, gamma	approved; nutraceutical	Adenosine monophosphate
DB00396	protein kinase, cAMP-dependent, catalytic, gamma	approved	Progesterone
DB00938	protein kinase, cAMP-dependent, catalytic, gamma	approved	Salmeterol

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Cross referenced IDs for PRKACG

* 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