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 PRKAR2B

Basic gene info.	Gene symbol	PRKAR2B
	Gene name	protein kinase, cAMP-dependent, regulatory, type II, beta
	Synonyms	PRKAR2\|RII-BETA
	Cytomap	UCSC genome browser: 7q22
	Genomic location	chr7 :106685177-106802256
	Type of gene	protein-coding
	RefGenes	NM_002736.2,
	Ensembl id	ENSG00000005249
	Description	H_RG363E19.2WUGSC:H_RG363E19.2cAMP-dependent protein kinase type II-beta regulatory chaincAMP-dependent protein kinase type II-beta regulatory subunit
	Modification date	20141207
dbXrefs	MIM : 176912
	HGNC : HGNC
	Ensembl : ENSG00000005249
	HPRD : 01486
	Vega : OTTHUMG00000137418
Protein	UniProt: P31323 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PRKAR2B
	BioGPS: 5577
	Gene Expression Atlas: ENSG00000005249
	The Human Protein Atlas: ENSG00000005249
Pathway	NCI Pathway Interaction Database: PRKAR2B
	KEGG: PRKAR2B
	REACTOME: PRKAR2B
	ConsensusPathDB
	Pathway Commons: PRKAR2B
Metabolism	MetaCyc: PRKAR2B
	HUMANCyc: PRKAR2B
Regulation	Ensembl's Regulation: ENSG00000005249
	miRBase: chr7 :106,685,177-106,802,256
	TargetScan: NM_002736
	cisRED: ENSG00000005249
Context	iHOP: PRKAR2B
	cancer metabolism search in PubMed: PRKAR2B
	UCL Cancer Institute: PRKAR2B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PRKAR2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PRKAR2B
	Familial Cancer Database: PRKAR2B

* 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

Others
OMIM	176912; gene.
Orphanet
Disease	KEGG Disease: PRKAR2B
	MedGen: PRKAR2B (Human Medical Genetics with Condition)
	ClinVar: PRKAR2B
Phenotype	MGI: PRKAR2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PRKAR2B

Mutations for PRKAR2B

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
liver	PRKAR2B	chr7	106795985	106795985	COG5	chr7	106894145	106894145

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 PRKAR2B 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
GW493216	PRKAR2B	18	131	7	106729510	106729633	RNF121	117	162	11	71664187	71664232
T06404	UNC5D	1	194	8	35317123	35317316	PRKAR2B	194	360	7	106689677	106689843

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=2)	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
chr7:106685448-106685448	p.A32A	4
chr7:106786832-106786832	p.E223*	3
chr7:106685560-106685560	p.P70S	2
chr7:106710728-106710728	p.P104A	2
chr7:106797436-106797436	p.S309L	2
chr7:106710740-106710740	p.R108*	2
chr7:106797452-106797452	p.F314F	2
chr7:106791406-106791406	p.A261S	2
chr7:106791470-106791470	p.?	2
chr7:106797673-106797673	p.R343*	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	1	1	3	1		2		2			1	4	1			6	7		2
# mutation	1	1	1	3	1		2		2			1	4	1			6	8		2
nonsynonymous SNV	1	1	1	3	1		2		2				2	1			4	7		1
synonymous SNV												1	2				2	1		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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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
chr7:106786820	p.G219R	2
chr7:106797434	p.R108Q	1
chr7:106710741	p.E223G	1
chr7:106786812	p.F109L	1
chr7:106797436	p.L247W	1
chr7:106710743	p.R112H	1
chr7:106797452	p.A261S	1
chr7:106710753	p.S164F	1
chr7:106786829	p.D299H	1
chr7:106797459	p.F171L	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 PRKAR2B 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 PRKAR2B

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


AFF3,AHCYL2,CRBN,DMXL1,EPB41L5,HBP1,ICA1L, KANSL3,MTMR10,NDFIP1,PCLO,PRKAR2B,PRLR,PTPLAD1, RSBN1L,SALL2,TAF9B,TLK1,TMEM209,UBN2,WASL	ACO1,AOC3,FAM213A,PQLC2L,CD36,EBF1,FAM89A, GYG2,HRASLS5,KCNIP2,MARC1,PCYOX1,PDE3B,PEX19, PLIN1,PPARG,PPP2R5A,PRKAR2B,RTN3,SIK2,UBA2

ABCA6,ABCD2,ACSM5,ADH1B,ARHGEF6,SMCO3,CD300LG, CD36,FABP4,GGTA1P,GNG2,HEPACAM,LOC339524,PDE1B, PI16,PLIN4,PRKAR2B,RBP7,SEMA3G,SGCG,TUSC5	ANXA1,ARL13B,TMEM263,CCDC169,C2orf74,CDK2AP1,CTPS1, FGF10,MFAP5,MTERF2,MYEF2,NFYB,PRKAR2B,PSMC3IP, RAD51D,RGS16,RSPO2,SCML2,TPD52L1,WBP4,ZNHIT6

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 PRKAR2B

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P31323; -.
Organism-specific databases	PharmGKB	PA33758; -.
Organism-specific databases	CTD	5577; -.

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

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Cross referenced IDs for PRKAR2B

* 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