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 PPP2R1B

Basic gene info.	Gene symbol	PPP2R1B
	Gene name	protein phosphatase 2, regulatory subunit A, beta
	Synonyms	PP2A-Abeta\|PR65B
	Cytomap	UCSC genome browser: 11q23.2
	Genomic location	chr11 :111597631-111637169
	Type of gene	protein-coding
	RefGenes	NM_001177562.1, NM_001177563.1,NM_002716.4,NM_181699.2,NM_181700.1,
	Ensembl id	ENSG00000262764
	Description	PP2A, subunit A, PR65-beta isoformPP2A, subunit A, R1-beta isoformprotein phosphatase 2 (formerly 2A), regulatory subunit A, beta isoformprotein phosphatase 2, structural/regulatory subunit A, betaserine/threonine-protein phosphatase 2A 65 kDa regulat
	Modification date	20141207
dbXrefs	MIM : 603113
	HGNC : HGNC
	Ensembl : ENSG00000137713
	HPRD : 04384
	Vega : OTTHUMG00000166741
Protein	UniProt: P30154 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2R1B
	BioGPS: 5519
	Gene Expression Atlas: ENSG00000262764
	The Human Protein Atlas: ENSG00000262764
Pathway	NCI Pathway Interaction Database: PPP2R1B
	KEGG: PPP2R1B
	REACTOME: PPP2R1B
	ConsensusPathDB
	Pathway Commons: PPP2R1B
Metabolism	MetaCyc: PPP2R1B
	HUMANCyc: PPP2R1B
Regulation	Ensembl's Regulation: ENSG00000262764
	miRBase: chr11 :111,597,631-111,637,169
	TargetScan: NM_001177562
	cisRED: ENSG00000262764
Context	iHOP: PPP2R1B
	cancer metabolism search in PubMed: PPP2R1B
	UCL Cancer Institute: PPP2R1B
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PPP2R1B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2R1B
	Familial Cancer Database: PPP2R1B

* 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_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	603113; gene. 603113; gene.
Orphanet
Disease	KEGG Disease: PPP2R1B
	MedGen: PPP2R1B (Human Medical Genetics with Condition)
	ClinVar: PPP2R1B
Phenotype	MGI: PPP2R1B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2R1B

Mutations for PPP2R1B

* 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 PPP2R1B 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
BG562569	TAT	1	339	16	71601286	71601625	PPP2R1B	333	781	11	111610550	111611006
BQ329687	PPP2R1B	18	114	11	111610247	111610344	NHP2L1	108	366	22	42070195	42070449
BE564406	LAD1	1	62	1	201355560	201355621	PPP2R1B	50	596	11	111611769	111612317

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=36)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr11:111613292-111613292	p.N551S	2
chr11:111618707-111618707	p.S457F	2
chr11:111614213-111614213	p.L481V	2
chr11:111612831-111612831	p.L579L	2
chr11:111624171-111624171	p.D387G	2
chr11:111626047-111626047	p.R272H	1
chr11:111612842-111612842	p.V575A	1
chr11:111631733-111631733	p.R117C	1
chr11:111618706-111618706	p.S457S	1
chr11:111624212-111624212	p.T373T	1

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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	4		1	5	2		2		4			7	3	1	1		3	7	1	5
# mutation	4		1	5	2		2		4			9	3	1	1		3	8	1	7
nonsynonymous SNV	3			4	2		2		1			5	2	1	1		3	4		5
synonymous SNV	1		1	1					3			4	1					4	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
chr11:111618707	p.L452L,PPP2R1B	2
chr11:111612831	p.R184R,PPP2R1B	2
chr11:111625731	p.S330F,PPP2R1B	2
chr11:111636068	p.R143H,PPP2R1B	1
chr11:111614250	p.E594K,PPP2R1B	1
chr11:111624289	p.I309I,PPP2R1B	1
chr11:111626053	p.L296L,PPP2R1B	1
chr11:111597721	p.R106C,PPP2R1B	1
chr11:111636081	p.L587L,PPP2R1B	1
chr11:111618706	p.I269M,PPP2R1B	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 PPP2R1B 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 PPP2R1B

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


ALDOB,ALG9,ANKFN1,ARCN1,C11orf57,SPX,CHRNA2, CPE,DAAM2,DLAT,ENAM,GNMT,KCTD4,NR5A1, PPP2R1B,PRKACB,SAMD13,SIK2,SMOC2,UCN3,ZNF836	APOL6,CLMP,ASPA,BTD,DMGDH,DOCK11,EHBP1, FERMT2,GLYAT,HRASLS5,LAMA4,LOC339524,MMD,MRAS, PALMD,PPP2R1B,SAR1A,SEPT11,SORBS1,TSPAN3,VKORC1L1

AASDHPPT,ALG9,C11orf54,C11orf57,CHEK1,CUL5,DLAT, EED,FAM76B,MPZL2,NPAT,NUP160,PPP2R1B,PPP6R3, SC5D,SDHD,THUMPD3,TMEM135,UBE4A,USP28,ZW10	ACTR2,AP1G1,CDH17,CEBPG,CMAS,CORO2A,EPCAM, F11R,GPD2,KIF16B,LIMA1,MYO6,NIPA2,PDCD6IP, PPP2R1B,RAB14,RBM47,RNF6,PTBP3,VDAC1,YWHAB

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 PPP2R1B

There's no related Drug.

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Cross referenced IDs for PPP2R1B

* 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