Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 RPIA
Basic gene info.Gene symbolRPIA
Gene nameribose 5-phosphate isomerase A
SynonymsRPI
CytomapUCSC genome browser: 2p11.2
Genomic locationchr2 :88991175-89050452
Type of geneprotein-coding
RefGenesNM_144563.2,
Ensembl idENSG00000153574
Descriptionphosphoriboisomeraseribose 5-phosphate epimeraseribose-5-phosphate isomerase
Modification date20141207
dbXrefs MIM : 180430
HGNC : HGNC
Ensembl : ENSG00000153574
HPRD : 01589
Vega : OTTHUMG00000130333
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPIA
BioGPS: 22934
Gene Expression Atlas: ENSG00000153574
The Human Protein Atlas: ENSG00000153574
PathwayNCI Pathway Interaction Database: RPIA
KEGG: RPIA
REACTOME: RPIA
ConsensusPathDB
Pathway Commons: RPIA
MetabolismMetaCyc: RPIA
HUMANCyc: RPIA
RegulationEnsembl's Regulation: ENSG00000153574
miRBase: chr2 :88,991,175-89,050,452
TargetScan: NM_144563
cisRED: ENSG00000153574
ContextiHOP: RPIA
cancer metabolism search in PubMed: RPIA
UCL Cancer Institute: RPIA
Assigned class in ccmGDBC

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

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

Mutations for RPIA
* 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 RPIA 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=26)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr2:89035244-89035244p.A196T3
chr2:89035207-89035207p.K183N2
chr2:88999546-88999546p.E122D2
chr2:89028845-89028845p.R151Q1
chr2:89049589-89049589p.F310F1
chr2:89035255-89035255p.?1
chr2:88991244-88991244p.L10I1
chr2:89037542-89037542p.D263H1
chr2:89034083-89034083p.I159I1
chr2:89036060-89036060p.S202L1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2116  2 1  411  22 6
# mutation2115  2 1  411  22 7
nonsynonymous SNV2  3  1    4 1   1 7
synonymous SNV 112  1 1   1   21  
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
chr2:89035244p.A196T4
chr2:89035207p.E122D2
chr2:88999546p.K183N2
chr2:89037549p.S27S1
chr2:88991297p.G212V1
chr2:89035238p.G86G1
chr2:89049502p.I215I1
chr2:88991474p.G235G1
chr2:89049506p.C128C1
chr2:89035252p.V249A1

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 RPIA 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 RPIA

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

AURKB,BCL11A,CDC20,CDCA3,CDCA8,CENPA,FAM136A,
KCMF1,KIF2C,LYAR,MAGOH,MRPS5,NDUFAF4,NOP58,
RBM17,RPIA,SF3B14,SNRPD1,SNRPG,UBE2C,USP39
SLIRP,C14orf2,COA6,SMIM20,MALSU1,TMEM261,CCDC58,
COX7C,CWC15,LAMTOR5,MRPS24,MTX2,NDUFA12,NDUFB1,
PCBP1,PDCD2L,PDCD5,RPIA,EMC4,TPT1,UQCRB

ATIC,CAMKMT,CDCA7,CIAO1,DARS,METTL5,NIFK,
NOL10,NUFIP1,PDCL3,PIGU,PNO1,RNASEH2B,RPF2,
RPIA,SMYD5,SSB,TOMM34,TSN,USP39,WDR12
B4GALT3,CFTR,DCAF12,DUS1L,GSS,KCNN4,MCCC1,
MCCC2,MTIF2,NDUFA10,PIGU,PODXL2,PPP1R1B,RPIA,
SLC25A10,SLC35A4,SMAGP,STARD7,SUPV3L1,TUFM,UNG
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 RPIA
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
DB02053ribose 5-phosphate isomerase AexperimentalRibose-5-Phosphate
DB03745ribose 5-phosphate isomerase AexperimentalArabinose-5-Phosphate
DB04127ribose 5-phosphate isomerase AexperimentalBeta-D-Arabinofuranose-5'-Phosphate
DB04272ribose 5-phosphate isomerase AexperimentalCitric Acid


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Cross referenced IDs for RPIA
* 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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