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 MPI

Basic gene info.	Gene symbol	MPI
	Gene name	mannose phosphate isomerase
	Synonyms	CDG1B\|PMI\|PMI1
	Cytomap	UCSC genome browser: 15q24.1
	Genomic location	chr15 :75182409-75190565
	Type of gene	protein-coding
	RefGenes	NM_001289155.1, NM_001289156.1,NM_001289157.1,NM_002435.2,
	Ensembl id	ENSG00000178802
	Description	mannose-6-phosphate isomerasephosphohexomutasephosphomannose isomerase 1
	Modification date	20141219
dbXrefs	MIM : 154550
	HGNC : HGNC
	Ensembl : ENSG00000178802
	HPRD : 01108
	Vega : OTTHUMG00000142826
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MPI
	BioGPS: 4351
	Gene Expression Atlas: ENSG00000178802
	The Human Protein Atlas: ENSG00000178802
Pathway	NCI Pathway Interaction Database: MPI
	KEGG: MPI
	REACTOME: MPI
	ConsensusPathDB
	Pathway Commons: MPI
Metabolism	MetaCyc: MPI
	HUMANCyc: MPI
Regulation	Ensembl's Regulation: ENSG00000178802
	miRBase: chr15 :75,182,409-75,190,565
	TargetScan: NM_001289155
	cisRED: ENSG00000178802
Context	iHOP: MPI
	cancer metabolism search in PubMed: MPI
	UCL Cancer Institute: MPI
Assigned class in ccmGDB	C

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

Cancer 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/

Metabolic Pathway Description
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM REACTOME_METABOLISM_OF_PROTEINS

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

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MPI 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

There's no copy number variation information in COSMIC data for this gene.

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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=3

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Somatic 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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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
chr15:75189370-75189370	p.A288V	3
chr15:75188521-75188521	p.I233I	2
chr15:75189523-75189523	p.D339G	1
chr15:75182874-75182874	p.P8Q	1
chr15:75185067-75185067	p.E137D	1
chr15:75188528-75188528	p.E236K	1
chr15:75189523-75189524	p.V342fs*17	1
chr15:75182890-75182890	p.V13V	1
chr15:75185068-75185068	p.M138V	1
chr15:75188574-75188574	p.C251Y	1

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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	2	3		3			1		2			3	2	2			1	2		7
# mutation	2	3		3			1		2			4	2	2			1	2		8
nonsynonymous SNV	1	2		3			1		1			2	1	1			1	2		5
synonymous SNV	1	1							1			2	1	1						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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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
chr15:75188494	p.A174A,MPI	2
chr15:75188521	p.I183I,MPI	2
chr15:75189523	p.S34S,MPI	1
chr15:75182890	p.G215V,MPI	1
chr15:75185540	p.R15H,MPI	1
chr15:75189853	p.S240L,MPI	1
chr15:75182953	p.L47L,MPI	1
chr15:75189909	p.L275L,MPI	1
chr15:75183769	p.D81N,MPI	1
chr15:75189916	p.R278Q,MPI	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 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

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


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

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 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