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 PKLR

Basic gene info.	Gene symbol	PKLR
	Gene name	pyruvate kinase, liver and RBC
	Synonyms	PK1\|PKL\|PKR\|PKRL\|RPK
	Cytomap	UCSC genome browser: 1q21
	Genomic location	chr1 :155259083-155271225
	Type of gene	protein-coding
	RefGenes	NM_000298.5, NM_181871.3,
	Ensembl id	ENSG00000262785
	Description	R-type/L-type pyruvate kinasepyruvate kinase 1pyruvate kinase PKLRpyruvate kinase isozyme R/Lpyruvate kinase isozymes L/Rpyruvate kinase isozymes R/Lpyruvate kinase type Lpyruvate kinase, liver and blood cellred cell/liver pyruvate kinase
	Modification date	20141207
dbXrefs	MIM : 609712
	HGNC : HGNC
	Ensembl : ENSG00000143627
	HPRD : 11841
	Vega : OTTHUMG00000035875
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PKLR
	BioGPS: 5313
	Gene Expression Atlas: ENSG00000262785
	The Human Protein Atlas: ENSG00000262785
Pathway	NCI Pathway Interaction Database: PKLR
	KEGG: PKLR
	REACTOME: PKLR
	ConsensusPathDB
	Pathway Commons: PKLR
Metabolism	MetaCyc: PKLR
	HUMANCyc: PKLR
Regulation	Ensembl's Regulation: ENSG00000262785
	miRBase: chr1 :155,259,083-155,271,225
	TargetScan: NM_000298
	cisRED: ENSG00000262785
Context	iHOP: PKLR
	cancer metabolism search in PubMed: PKLR
	UCL Cancer Institute: PKLR
Assigned class in ccmGDB	C

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

Cancer Description
Cancer	CGAP: PKLR
	Familial Cancer Database: PKLR

* 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
KEGG_GLYCOLYSIS_GLUCONEOGENESIS KEGG_PURINE_METABOLISM KEGG_PYRUVATE_METABOLISM BIOCARTA_GLYCOLYSIS_PATHWAY REACTOME_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

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

Mutations for PKLR

* 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	PKLR	chr1	155270488	155270508		chr1	155062638	155062658

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 PKLR 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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=54)	Stat. for Synonymous SNVs (# total SNVs=17)

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
chr1:155265256-155265256	p.P160Q	3
chr1:155265010-155265010	p.A197A	3
chr1:155265524-155265524	p.R103S	2
chr1:155264349-155264349	p.V297I	2
chr1:155263347-155263347	p.T384M	2
chr1:155263135-155263135	p.?	2
chr1:155264147-155264147	p.G332V	2
chr1:155261669-155261669	p.S499F	2
chr1:155264362-155264362	p.S292S	2
chr1:155264172-155264172	p.D324N	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	3		12	2		1		1			15	6	1			11	11	1	5
# mutation	1	3		13	2		1		1			15	6	1			12	11	1	7
nonsynonymous SNV	1	3		6	1		1		1			14	3	1			8	5		5
synonymous SNV				7	1							1	3				4	6	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
chr1:155264372	p.R289Q,PKLR	3
chr1:155263259	p.R289W,PKLR	2
chr1:155264362	p.A417A,PKLR	2
chr1:155264373	p.D324N,PKLR	2
chr1:155264172	p.F413F,PKLR	2
chr1:155263247	p.S292S,PKLR	2
chr1:155264938	p.Q353H,PKLR	1
chr1:155264135	p.P160Q,PKLR	1
chr1:155265336	p.C467W,PKLR	1
chr1:155271182	p.F350F,PKLR	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 PKLR 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 PKLR

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


ALKBH6,BLOC1S1,LAMTOR4,CCDC12,CCDC24,EGFL8,MZT2B, GUCY2EP,KRTAP12-4,LOC100271831,LOC100288778,MAGIX,MGMT,MRPL55, NDUFA13,NENF,PKLR,RFXANK,TMEM160,UCN,WASH3P	AIFM3,TEX43,ARRDC1-AS1,CCDC130,CEMP1,DCST1,FOXH1, HES7,LOC100130386,LOC644172,ASMTL-AS1,PAQR6,PKLR,RAB24, RETNLB,SCGB1D1,TBC1D3B,TCP10,TEKT4,WASH2P,WASH3P

AATF,ABCC2,ACACA,AGT,CCNE1,CISD3,DDX52, FAH,FXYD2,GLOD5,KCNA10,MRPL45,PKLR,QPRT, RGSL1,SLC22A12,SLC23A1,SNAR-A2,STARD3,TSPAN33,TTTY7	ACE2,ALPI,SMIM24,CYP4A11,CYP4F2,DAK,DHDH, FADS6,G6PC,HSD3B1,MS4A10,NAALADL1,NAT8B,NLRP6, PKLR,SLC13A1,SLC15A1,SLC23A1,SLC6A19,SLC6A4,XPNPEP2

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 PKLR

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
DB00119	pyruvate kinase, liver and RBC	approved; nutraceutical	Pyruvic acid
DB02726	pyruvate kinase, liver and RBC	experimental	2-Phosphoglycolic Acid
DB04551	pyruvate kinase, liver and RBC	experimental	Fructose-1,6-Diphosphate
DB00131	pyruvate kinase, liver and RBC	approved; nutraceutical	Adenosine monophosphate
DB00171	pyruvate kinase, liver and RBC	approved; nutraceutical	Adenosine triphosphate
DB00630	pyruvate kinase, liver and RBC	approved	Alendronate
DB00710	pyruvate kinase, liver and RBC	approved; investigational	Ibandronate
DB00282	pyruvate kinase, liver and RBC	approved	Pamidronate
DB00884	pyruvate kinase, liver and RBC	approved; investigational	Risedronate
DB00399	pyruvate kinase, liver and RBC	approved	Zoledronate

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Cross referenced IDs for PKLR

* 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