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 GPI
Basic gene info.Gene symbolGPI
Gene nameglucose-6-phosphate isomerase
SynonymsAMF|GNPI|NLK|PGI|PHI|SA-36|SA36
CytomapUCSC genome browser: 19q13.1
Genomic locationchr19 :34856031-34893318
Type of geneprotein-coding
RefGenesNM_000175.3,
NM_001184722.1,NM_001289789.1,NM_001289790.1,
Ensembl idENSG00000105220
Descriptionautocrine motility factorglucose phosphate isomerasehexose monophosphate isomerasehexosephosphate isomeraseneuroleukinoxoisomerasephosphoglucose isomerasephosphohexomutasephosphohexose isomerasephosphosaccharomutasesperm antigen 36sperm antigen
Modification date20141207
dbXrefs MIM : 172400
HGNC : HGNC
Ensembl : ENSG00000105220
HPRD : 01394
Vega : OTTHUMG00000182087
ProteinUniProt: P06744
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPI
BioGPS: 2821
Gene Expression Atlas: ENSG00000105220
The Human Protein Atlas: ENSG00000105220
PathwayNCI Pathway Interaction Database: GPI
KEGG: GPI
REACTOME: GPI
ConsensusPathDB
Pathway Commons: GPI
MetabolismMetaCyc: GPI
HUMANCyc: GPI
RegulationEnsembl's Regulation: ENSG00000105220
miRBase: chr19 :34,856,031-34,893,318
TargetScan: NM_000175
cisRED: ENSG00000105220
ContextiHOP: GPI
cancer metabolism search in PubMed: GPI
UCL Cancer Institute: GPI
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of GPI in cancer cell metabolism1. Niinaka Y, Harada K, Fujimuro M, Oda M, Haga A, et al. (2010) Silencing of autocrine motility factor induces mesenchymal-to-epithelial transition and suppression of osteosarcoma pulmonary metastasis. Cancer Res 70: 9483-9493. doi: 10.1158/0008-5472.CAN-09-3880. pmid: 2982894. go to article
2. Lin LL, Hsia CR, Hsu CL, Huang HC, Juan HF (2015) Integrating transcriptomics and proteomics to show that tanshinone IIA suppresses cell growth by blocking glucose metabolism in gastric cancer cells. BMC Genomics 16: 41. doi: 10.1186/s12864-015-1230-0. pmid: 4328042. go to article
3. Zou W, Al-Rubeai M (2015) Understanding central carbon metabolism of rapidly proliferating mammalian cells based on analysis of key enzymatic activities in GS-CHO cell lines. Biotechnol Appl Biochem. doi: 10.1002/bab.1409. go to article
4. Kim HR, Roe JS, Lee JE, Cho EJ, Youn HD (2013) p53 regulates glucose metabolism by miR-34a. Biochem Biophys Res Commun 437: 225-231. doi: 10.1016/j.bbrc.2013.06.043. go to article

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Phenotypic Information for GPI(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: GPI
Familial Cancer Database: GPI
* 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_STARCH_AND_SUCROSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
BIOCARTA_GLYCOLYSIS_PATHWAY
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 172400; gene.
613470; phenotype.
Orphanet 712; Hemolytic anemia due to glucophosphate isomerase deficiency.
DiseaseKEGG Disease: GPI
MedGen: GPI (Human Medical Genetics with Condition)
ClinVar: GPI
PhenotypeMGI: GPI (International Mouse Phenotyping Consortium)
PhenomicDB: GPI

Mutations for GPI
* 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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
breastGPIchr193486039134860391GPIchr193487387434873874
pancreasGPIchr193489302934893049chr194325312343253143
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows GPI related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample21 1             
GAIN (# sample)21 1             
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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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=41)
Stat. for Synonymous SNVs
(# total SNVs=18)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr19:34890129-34890129p.F429F3
chr19:34884178-34884178p.W277*2
chr19:34887543-34887543p.R417Q2
chr19:34890861-34890861p.A533S2
chr19:34859562-34859562p.M119I2
chr19:34884959-34884959p.A350A2
chr19:34868642-34868642p.G163G2
chr19:34856216-34856216p.Q15Q2
chr19:34890536-34890536p.A492T1
chr19:34859508-34859508p.V101V1

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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
# sample41 11  2 2  7531 55 6
# mutation41 10  2 2  8431 65 7
nonsynonymous SNV21 5  2 1  642  35 6
synonymous SNV2  5    1  2111 3  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
chr19:34857274p.R245S,GPI2
chr19:34884165p.F401L,GPI2
chr19:34856216p.Q15Q,GPI2
chr19:34884959p.A322A,GPI2
chr19:34890129p.G49G,GPI2
chr19:34890140p.S160F,GPI1
chr19:34859597p.Y335H,GPI1
chr19:34868784p.K57N,GPI1
chr19:34887209p.S160S,GPI1
chr19:34890524p.S339P,GPI1

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 GPI 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 GPI

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

ATP5G3,BOLA3,COX6B1,ENO1,GAPDH,GPI,LSR,
MRPS5,PDCD2L,PDCD5,PDHA1,PFKP,PGAM1,PKM,
PSMB2,TIMM50,TMEM147,TPI1,TUBA1C,UQCRH,UQCRHL
ACAA2,ACOT1,ACOT2,ACSS2,AKT2,ANXA6,ATP5G3,
BTBD6,NATD1,MROH8,CS,DLST,EIF2B3,GPI,
HSDL2,ITGA7,PDHA1,PFKFB1,PPP1R1A,RNF157,TESK1

ALDOA,ATP5B,BCAT2,CS,EIF3K,ENO1,FBL,
GAPDH,GPI,GYS1,HSPBP1,IMMT,PGAM1,RDH13,
RUVBL2,SARS2,SNRPA,TOMM40,TPI1,UBE2S,UQCRFS1
DAZAP1,DDB1,EIF3B,ELAVL1,FOXM1,GANAB,GPI,
HNRNPM,KHSRP,LMNB2,LONP1,MED24,MTHFD1,NOC2L,
RANGAP1,RNF26,TBCD,TBL3,TMEM201,USP5,VARS
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 GPI
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28841; -.
Organism-specific databasesCTD 2821; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02007glucose-6-phosphate isomeraseexperimentalAlpha-D-Glucose-6-Phosphate
DB02076glucose-6-phosphate isomeraseexperimental6-Phosphogluconic Acid
DB02093glucose-6-phosphate isomeraseexperimental5-Phospho-D-Arabinohydroxamic Acid
DB02548glucose-6-phosphate isomeraseexperimentalSorbitol 6-phosphate
DB03042glucose-6-phosphate isomeraseexperimental5-Phosphoarabinonic Acid
DB03581glucose-6-phosphate isomeraseexperimentalGlucose-6-Phosphate
DB03937glucose-6-phosphate isomeraseexperimentalErythose-4-Phosphate
DB04493glucose-6-phosphate isomeraseexperimentalFructose-6-Phosphate
DB00121glucose-6-phosphate isomeraseapproved; nutraceuticalBiotin


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Cross referenced IDs for GPI
* 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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