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 PCK2
Basic gene info.Gene symbolPCK2
Gene namephosphoenolpyruvate carboxykinase 2 (mitochondrial)
SynonymsPEPCK|PEPCK-M|PEPCK2
CytomapUCSC genome browser: 14q11.2
Genomic locationchr14 :24563482-24569770
Type of geneprotein-coding
RefGenesNM_001018073.2,
NM_001291556.1,NM_004563.3,
Ensembl idENSG00000100889
DescriptionPEP carboxykinasephosphoenolpyruvate carboxykinase [GTP], mitochondrialphosphopyruvate carboxylase
Modification date20141207
dbXrefs MIM : 614095
HGNC : HGNC
Ensembl : ENSG00000100889
HPRD : 02026
Vega : OTTHUMG00000028791
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PCK2
BioGPS: 5106
Gene Expression Atlas: ENSG00000100889
The Human Protein Atlas: ENSG00000100889
PathwayNCI Pathway Interaction Database: PCK2
KEGG: PCK2
REACTOME: PCK2
ConsensusPathDB
Pathway Commons: PCK2
MetabolismMetaCyc: PCK2
HUMANCyc: PCK2
RegulationEnsembl's Regulation: ENSG00000100889
miRBase: chr14 :24,563,482-24,569,770
TargetScan: NM_001018073
cisRED: ENSG00000100889
ContextiHOP: PCK2
cancer metabolism search in PubMed: PCK2
UCL Cancer Institute: PCK2
Assigned class in ccmGDBC

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Phenotypic Information for PCK2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PCK2
Familial Cancer Database: PCK2
* 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/

check002.gifMetabolic Pathway Description
KEGG_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_PYRUVATE_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PCK2
MedGen: PCK2 (Human Medical Genetics with Condition)
ClinVar: PCK2
PhenotypeMGI: PCK2 (International Mouse Phenotyping Consortium)
PhenomicDB: PCK2

Mutations for PCK2
* 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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PCK2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
There's no copy number variation information in COSMIC data for this gene.

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check002.gifSNV 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr14:24567582-24567582p.P149L2
chr14:24572402-24572402p.R469L2
chr14:24571977-24571977p.C417F2
chr14:24568857-24568857p.R315W2
chr14:24568928-24568928p.E338D2
chr14:24572012-24572012p.R429C2
chr14:24572735-24572735p.H495H2
chr14:24568323-24568323p.R244W2
chr14:24569275-24569275p.P363S1
chr14:24573119-24573119p.P623P1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample15 61 4 21 31  15818
# mutation15 61 4 21 31  15818
nonsynonymous SNV13 5  3 21 31  14617
synonymous SNV 2 11 1         12 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr14:24568928p.E338D,PCK22
chr14:24572402p.P291H,PCK21
chr14:24566131p.R335H,PCK21
chr14:24567684p.G20G,PCK21
chr14:24573040p.R315W,PCK21
chr14:24569335p.R345C,PCK21
chr14:24572431p.H50Y,PCK21
chr14:24566219p.R53R,PCK21
chr14:24567693p.G327V,PCK21
chr14:24573072p.R345H,PCK21

check002.gifOther 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

check002.gifCopy Number for PCK2 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 PCK2

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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

ACSF2,ACSM1,ALDH4A1,AP1G2,C15orf43,DCAF11,DHRS4,
DHRS4L2,EMC9,GCM1,MDP1,MVK,NEDD8,NRL,
PCK2,PSME1,RABGGTA,RNF31,TM9SF1,TMIGD1,UGT3A2
ADH1A,ANKRD53,ASS1,APMAP,CALCRL,CIDEA,CYP1A2,
DNAH9,ECHDC3,GLUL,GLYCTK,MOCS1,MOGAT1,ORMDL3,
PC,PCK1,PCK2,PCYT2,PMM1,PXMP2,TM7SF2

ADCK1,APEX1,ATP5S,C14orf166,COQ6,DCAF11,DHRS4,
DHRS4L2,GLRX5,HAUS4,HOMEZ,HSD17B8,ISCA2,NGDN,
OXA1L,PCK2,PSMB5,SETD3,TIMM9,TMEM55B,VTI1B
ACE2,ALPI,ANPEP,TMEM253,CHN2,CYP2J2,DGAT1,
GBA3,SLC52A1,MMEL1,MS4A8,MYO1A,NAT8B,OIT3,
PCK2,PKLR,PLCB3,PTGR1,SLC23A1,TM6SF2,AGMO
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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 PCK2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00121phosphoenolpyruvate carboxykinase 2 (mitochondrial)approved; nutraceuticalBiotin


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Cross referenced IDs for PCK2
* 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



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