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 PPP2R5D

Basic gene info.	Gene symbol	PPP2R5D
	Gene name	protein phosphatase 2, regulatory subunit B', delta
	Synonyms	B56D
	Cytomap	UCSC genome browser: 6p21.1
	Genomic location	chr6 :42952329-42980080
	Type of gene	protein-coding
	RefGenes	NM_001270476.1, NM_006245.3,NM_180976.2,NM_180977.2,
	Ensembl id	ENSG00000112640
	Description	PP2A B subunit isoform B'-deltaPP2A B subunit isoform B56-deltaPP2A B subunit isoform PR61-deltaPP2A B subunit isoform R5-deltaPP2A, B subunit, B' delta isoformPP2A, B subunit, B56 delta isoformPP2A, B subunit, PR61 delta isoformPP2A, B subunit, R5
	Modification date	20141207
dbXrefs	MIM : 601646
	HGNC : HGNC
	Ensembl : ENSG00000112640
	HPRD : 09039
	Vega : OTTHUMG00000014716
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2R5D
	BioGPS: 5528
	Gene Expression Atlas: ENSG00000112640
	The Human Protein Atlas: ENSG00000112640
Pathway	NCI Pathway Interaction Database: PPP2R5D
	KEGG: PPP2R5D
	REACTOME: PPP2R5D
	ConsensusPathDB
	Pathway Commons: PPP2R5D
Metabolism	MetaCyc: PPP2R5D
	HUMANCyc: PPP2R5D
Regulation	Ensembl's Regulation: ENSG00000112640
	miRBase: chr6 :42,952,329-42,980,080
	TargetScan: NM_001270476
	cisRED: ENSG00000112640
Context	iHOP: PPP2R5D
	cancer metabolism search in PubMed: PPP2R5D
	UCL Cancer Institute: PPP2R5D
Assigned class in ccmGDB	C

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Phenotypic Information for PPP2R5D(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2R5D
	Familial Cancer Database: PPP2R5D

* 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
Orphanet
Disease	KEGG Disease: PPP2R5D
	MedGen: PPP2R5D (Human Medical Genetics with Condition)
	ClinVar: PPP2R5D
Phenotype	MGI: PPP2R5D (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2R5D

Mutations for PPP2R5D

* 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
pancreas	PPP2R5D	chr6	42968756	42968776		chr6	46757961	46757981

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 PPP2R5D 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

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=35)	Stat. for Synonymous SNVs (# total SNVs=15)

Stat. for Deletions (# total SNVs=2)	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
chr6:42975737-42975737	p.R264H	2
chr6:42975745-42975745	p.G267S	2
chr6:42974938-42974938	p.S176*	2
chr6:42957352-42957352	p.K13fs*94	2
chr6:42974675-42974675	p.L117L	2
chr6:42977143-42977143	p.I445I	2
chr6:42975942-42975942	p.F287F	2
chr6:42974777-42974777	p.E151K	1
chr6:42977074-42977074	p.A422A	1
chr6:42978631-42978631	p.R523*	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=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	2	3	1	6	1		3		1			5		1		1	1	6		11
# mutation	2	3	1	6	1		3		1			6		1		1	1	6		12
nonsynonymous SNV	1	2		4			3					5		1			1	3		8
synonymous SNV	1	1	1	2	1				1			1				1		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
chr6:42975737	p.R158H,PPP2R5D	3
chr6:42974675	p.L11L,PPP2R5D	2
chr6:42975175	p.T490T,PPP2R5D	1
chr6:42976451	p.E45D,PPP2R5D	1
chr6:42974730	p.I202I,PPP2R5D	1
chr6:42978669	p.R54C,PPP2R5D	1
chr6:42975223	p.R219S,PPP2R5D	1
chr6:42976473	p.D55N,PPP2R5D	1
chr6:42974732	p.Q243Q,PPP2R5D	1
chr6:42978683	p.R75Q,PPP2R5D	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 PPP2R5D 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 PPP2R5D

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


AARS2,ABCC10,RRP36,CDC5L,CUL7,GTPBP2,HSP90AB1, KLHDC3,MEA1,MED20,MRPS10,MRPS18A,NFYA,POLH, POLR1C,PPP2R5D,SLC29A1,SLC35B2,TJAP1,XPO5,ZNF318	AP2A1,ATG9A,APOPT1,NATD1,C21orf33,DLST,FZD9, GPI,HADHA,HDLBP,PACS2,GATB,PPP2R5D,PRKACA, PSMD2,SAMM50,SLC25A23,SLC6A8,ST3GAL3,VPS4A,WBSCR16

AARS2,BYSL,RRP36,ZC2HC1B,CCND3,CDCA3,CLDN25, F11,KLHDC3,MAD2L1BP,MEA1,MED20,MRPL2,PPP2R5D, RHAG,SRF,TAF8,TJAP1,TOMM6,XPO5,ZNF318	ABHD6,ANPEP,ADIRF,GBA3,GCNT4,GNB1,SLC52A1, HEBP1,HOXC11,HOXC6,HOXC8,ING2,LOC148709,MARC2, MSRA,PPP2R5D,PTGR1,SPAM1,SUSD2,AGMO,TTBK1

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 PPP2R5D

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00675	protein phosphatase 2, regulatory subunit B', delta	approved	Tamoxifen
DB01394	protein phosphatase 2, regulatory subunit B', delta	approved	Colchicine
DB00864	protein phosphatase 2, regulatory subunit B', delta	approved; investigational	Tacrolimus
DB00877	protein phosphatase 2, regulatory subunit B', delta	approved; investigational	Sirolimus
DB00131	protein phosphatase 2, regulatory subunit B', delta	approved; nutraceutical	Adenosine monophosphate
DB00171	protein phosphatase 2, regulatory subunit B', delta	approved; nutraceutical	Adenosine triphosphate
DB00988	protein phosphatase 2, regulatory subunit B', delta	approved	Dopamine

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Cross referenced IDs for PPP2R5D

* 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