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 PRKACB

Basic gene info.	Gene symbol	PRKACB
	Gene name	protein kinase, cAMP-dependent, catalytic, beta
	Synonyms	PKA C-beta\|PKACB
	Cytomap	UCSC genome browser: 1p31.1
	Genomic location	chr1 :84543744-84670979
	Type of gene	protein-coding
	RefGenes	NM_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 id	ENSG00000142875
	Description	cAMP-dependent protein kinase catalytic beta subunit isoform 4abcAMP-dependent protein kinase catalytic subunit betaprotein kinase A catalytic subunit beta
	Modification date	20141207
dbXrefs	MIM : 176892
	HGNC : HGNC
	Ensembl : ENSG00000142875
	HPRD : 01482
	Vega : OTTHUMG00000009975
Protein	UniProt: P22694 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKACB
	BioGPS: 5567
	Gene Expression Atlas: ENSG00000142875
	The Human Protein Atlas: ENSG00000142875
Pathway	NCI Pathway Interaction Database: PRKACB
	KEGG: PRKACB
	REACTOME: PRKACB
	ConsensusPathDB
	Pathway Commons: PRKACB
Metabolism	MetaCyc: PRKACB
	HUMANCyc: PRKACB
Regulation	Ensembl's Regulation: ENSG00000142875
	miRBase: chr1 :84,543,744-84,670,979
	TargetScan: NM_001242857
	cisRED: ENSG00000142875
Context	iHOP: PRKACB
	cancer metabolism search in PubMed: PRKACB
	UCL Cancer Institute: PRKACB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PRKACB in cancer cell metabolism	1. 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

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

Cancer 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/

Metabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	176892; gene. 176892; gene.
Orphanet
Disease	KEGG Disease: PRKACB
	MedGen: PRKACB (Human Medical Genetics with Condition)
	ClinVar: PRKACB
Phenotype	MGI: PRKACB (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PRKACB	chr1	84555703	84555723	PRKACB	chr1	84565473	84565493

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)

Related fusion transcripts : go to Chitars2.0

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

ID	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
DA775505	NEUROD6	1	140	7	31380207	31380346	PRKACB	139	554	1	84644858	84662339
BF944829	PRKACB	58	270	1	84633057	84633274	RYR3	260	452	15	34021153	34023790
DA223586	SLC25A44	1	387	1	156163908	156169881	PRKACB	386	527	1	84630378	84630519

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=5

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Somatic 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)

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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
chr1:84663454-84663454	p.W197R	3
chr1:84649767-84649767	p.I95M	2
chr1:84644908-84644908	p.E32G	2
chr1:84649790-84649790	p.F103S	2
chr1:84662305-84662305	p.P142P	2
chr1:84700929-84700929	p.E333Q	2
chr1:84668371-84668371	p.Y216*	2
chr1:84647960-84647960	p.K62K	2
chr1:84668407-84668407	p.L228L	2
chr1:84679969-84679969	p.T300M	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=2

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			5			2		3			7	3	1			3	3		4
# mutation	1			4			2		3			8	3	1			3	3		4
nonsynonymous SNV	1			3			2		3			6	3	1			3	2		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])

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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
chr1:84644908	p.L215L,PRKACB	2
chr1:84700929	p.I216M,PRKACB	2
chr1:84668407	p.E20G,PRKACB	2
chr1:84668410	p.E320Q,PRKACB	2
chr1:84650823	p.G10V,PRKACB	1
chr1:84679841	p.H33Q	1
chr1:84610143	p.S21Y,PRKACB	1
chr1:84650847	p.M219I,PRKACB	1
chr1:84679863	p.A220V,PRKACB	1
chr1:84641485	p.P22S,PRKACB	1

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 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]

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Gene Expression for PRKACB

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


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

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 PRKACB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P22694; -.
Chemistry	ChEMBL	CHEMBL2918; -.
Chemistry	GuidetoPHARMACOLOGY	1477; -.
Chemistry	BindingDB	P22694; -.
Chemistry	ChEMBL	CHEMBL2918; -.
Chemistry	GuidetoPHARMACOLOGY	1477; -.
Organism-specific databases	PharmGKB	PA33749; -.
Organism-specific databases	PharmGKB	PA33749; -.
Organism-specific databases	CTD	5567; -.
Organism-specific databases	CTD	5567; -.

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, beta	approved; nutraceutical	L-Arginine
DB00155	protein kinase, cAMP-dependent, catalytic, beta	approved; nutraceutical	L-Citrulline
DB00435	protein kinase, cAMP-dependent, catalytic, beta	approved	Nitric Oxide
DB00988	protein kinase, cAMP-dependent, catalytic, beta	approved	Dopamine
DB00171	protein kinase, cAMP-dependent, catalytic, beta	approved; nutraceutical	Adenosine triphosphate
DB00770	protein kinase, cAMP-dependent, catalytic, beta	approved; investigational	Alprostadil
DB00668	protein kinase, cAMP-dependent, catalytic, beta	approved	Epinephrine
DB00131	protein kinase, cAMP-dependent, catalytic, beta	approved; nutraceutical	Adenosine monophosphate
DB00396	protein kinase, cAMP-dependent, catalytic, beta	approved	Progesterone
DB00938	protein kinase, cAMP-dependent, catalytic, beta	approved	Salmeterol

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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