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 MPI
Basic gene info.Gene symbolMPI
Gene namemannose phosphate isomerase
SynonymsCDG1B|PMI|PMI1
CytomapUCSC genome browser: 15q24.1
Genomic locationchr15 :75182409-75190565
Type of geneprotein-coding
RefGenesNM_001289155.1,
NM_001289156.1,NM_001289157.1,NM_002435.2,
Ensembl idENSG00000178802
Descriptionmannose-6-phosphate isomerasephosphohexomutasephosphomannose isomerase 1
Modification date20141219
dbXrefs MIM : 154550
HGNC : HGNC
Ensembl : ENSG00000178802
HPRD : 01108
Vega : OTTHUMG00000142826
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MPI
BioGPS: 4351
Gene Expression Atlas: ENSG00000178802
The Human Protein Atlas: ENSG00000178802
PathwayNCI Pathway Interaction Database: MPI
KEGG: MPI
REACTOME: MPI
ConsensusPathDB
Pathway Commons: MPI
MetabolismMetaCyc: MPI
HUMANCyc: MPI
RegulationEnsembl's Regulation: ENSG00000178802
miRBase: chr15 :75,182,409-75,190,565
TargetScan: NM_001289155
cisRED: ENSG00000178802
ContextiHOP: MPI
cancer metabolism search in PubMed: MPI
UCL Cancer Institute: MPI
Assigned class in ccmGDBC

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Phenotypic Information for MPI(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MPI
Familial Cancer Database: MPI
* 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_FRUCTOSE_AND_MANNOSE_METABOLISM
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM
REACTOME_METABOLISM_OF_PROTEINS

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

Mutations for MPI
* 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 MPI 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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr15:75189370-75189370p.A288V3
chr15:75188521-75188521p.I233I2
chr15:75185047-75185047p.D131N1
chr15:75190017-75190017p.L406L1
chr15:75188494-75188494p.A224A1
chr15:75182420-75182420p.A2A1
chr15:75189490-75189490p.R328Q1
chr15:75190052-75190052p.R418H1
chr15:75185065-75185065p.E137Q1
chr15:75182874-75182874p.P8Q1

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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
# sample23 3  1 2  322  12 7
# mutation23 3  1 2  422  12 8
nonsynonymous SNV12 3  1 1  211  12 5
synonymous SNV11      1  211     3
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
chr15:75188494p.A174A,MPI2
chr15:75188521p.I183I,MPI2
chr15:75185531p.E186K,MPI1
chr15:75189490p.P8Q,MPI1
chr15:75182874p.C201Y,MPI1
chr15:75185534p.V13V,MPI1
chr15:75189523p.N208S,MPI1
chr15:75182890p.S34S,MPI1
chr15:75185540p.G215V,MPI1
chr15:75189853p.R15H,MPI1

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 MPI 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 MPI

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

ARFIP2,BBS4,FAM219B,C15orf40,CYB5D2,FAM174B,G6PC3,
GHDC,HDDC3,HMGCL,IMP3,IVD,MPI,NDUFAF1,
P4HTM,PIGV,PNPLA4,SCAMP2,THTPA,UBL7,WDR73
ATP5SL,ATPAF2,BCKDK,RPP25L,COG4,ECSIT,ERAL1,
FAHD2B,KLHDC3,LRRC47,MPI,MRPL14,MRPS18B,MRPS9,
NDUFB11,NDUFV1,NT5M,RPUSD3,STOML2,TXN2,UBL7

GDPGP1,HYPK,CENPM,CHAC2,CLN6,DLST,GSTZ1,
IDH2,IDH3A,IMP3,IVD,LEO1,MPI,MRPS11,
MTHFS,PGAM1,PPCDC,SCAMP2,TIPIN,TK1,TTLL12
ACP2,ACSL5,LINC00483,GUCD1,C9orf40,DAPK2,DHRS11,
ESPN,GDPD2,HMOX1,LASP1,LOC151534,MPI,NAPRT,
PLEKHG6,SEPHS2,SLC9A3R1,SULT1A2,TMEM82,TOM1,ULK3
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 MPI


There's no related Drug.
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Cross referenced IDs for MPI
* 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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