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 MTMR3
Basic gene info.Gene symbolMTMR3
Gene namemyotubularin related protein 3
SynonymsFYVE-DSP1|ZFYVE10
CytomapUCSC genome browser: 22q12.2
Genomic locationchr22 :30279157-30426857
Type of geneprotein-coding
RefGenesNM_021090.3,
NM_153050.2,NM_153051.2,NM_001013676.1,
Ensembl idENSG00000100330
DescriptionFYVE (Fab1 YGLO23 Vsp27 EEA1 domain) dual-specificity protein phosphataseFYVE domain-containing dual specificity protein phosphatase 1myotubularin-related protein 3phosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphate pho
Modification date20141207
dbXrefs MIM : 603558
HGNC : HGNC
Ensembl : ENSG00000100330
HPRD : 09151
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTMR3
BioGPS: 8897
Gene Expression Atlas: ENSG00000100330
The Human Protein Atlas: ENSG00000100330
PathwayNCI Pathway Interaction Database: MTMR3
KEGG: MTMR3
REACTOME: MTMR3
ConsensusPathDB
Pathway Commons: MTMR3
MetabolismMetaCyc: MTMR3
HUMANCyc: MTMR3
RegulationEnsembl's Regulation: ENSG00000100330
miRBase: chr22 :30,279,157-30,426,857
TargetScan: NM_021090
cisRED: ENSG00000100330
ContextiHOP: MTMR3
cancer metabolism search in PubMed: MTMR3
UCL Cancer Institute: MTMR3
Assigned class in ccmGDBC

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Phenotypic Information for MTMR3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MTMR3
Familial Cancer Database: MTMR3
* 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_PHOSPHOLIPID_METABOLISM
REACTOME_PI_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MTMR3
MedGen: MTMR3 (Human Medical Genetics with Condition)
ClinVar: MTMR3
PhenotypeMGI: MTMR3 (International Mouse Phenotyping Consortium)
PhenomicDB: MTMR3

Mutations for MTMR3
* 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
ovaryMTMR3chr223037413730374157MTMR3chr223037094330370963
pancreasMTMR3chr223028750530287705chr223599959535999795
pancreasMTMR3chr223030124330301263NF2chr223005898130059001
pancreasMTMR3chr223033557230335592NEFHchr222987954729879567
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 MTMR3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG469920MTMR32124223027922630279348APOH124873176421298164225541
BG824141MTMR32178223027917230279348APOH178827176421667664225541
BE764648LOC2864671595X130942349130942428MTMR388262223042344430423618
T05096MTMR31105223030424230304346BRWD1105373214056034340560610

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 # sample1       2 1  11  
GAIN (# sample)1       1 1  11  
LOSS (# sample)        1        
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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=3)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=2)

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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
chr22:30416328-30416329p.Q894fs*82
chr22:30413924-30413924p.Y561Y1
chr22:30416336-30416338p.S897delS1
chr22:30387596-30387596p.H133Y1
chr22:30416522-30416522p.C958C1
chr22:30398972-30398972p.V221L1
chr22:30416779-30416779p.T1044I1
chr22:30403266-30403266p.R279*1
chr22:30416812-30416812p.R1055H1
chr22:30403893-30403893p.S294F1

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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
# sample53 111 1 311471  121317
# mutation53 121 1 311671  141319
nonsynonymous SNV53 81   1 147   10915
synonymous SNV   4  1 21 2 1  44 4
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
chr22:30415660p.C958C,MTMR32
chr22:30398934p.R671K,MTMR32
chr22:30416522p.S208T,MTMR32
chr22:30418071p.E724K,MTMR31
chr22:30394825p.V1133L,MTMR31
chr22:30405059p.R234H,MTMR31
chr22:30416049p.S538L,MTMR31
chr22:30413918p.S727T,MTMR31
chr22:30416562p.A959T,MTMR31
chr22:30418102p.D1149G,MTMR31

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 MTMR3 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 MTMR3

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

PRR14L,CBX6,CRKL,SPECC1L,DEPDC5,DUSP18,EIF4ENIF1,
EP300,HMGXB4,HPS4,KIAA1671,MAPK1,MTMR3,PEX26,
PI4KA,RNF185,SF3A1,TNRC6B,TUG1,ZC3H7B,ZNF70
AMOTL1,ASB1,CYB5RL,DDI2,HERC1,HUWE1,KIAA2018,
KIF13A,MTMR3,MTR,PRPF8,TSC1,UBE3B,UBR2,
UBR4,VPS13D,ZFYVE26,ZNF592,ZNF641,ZNF778,ZZEF1

AKAP13,BRD1,HECTD4,PRR14L,CRKL,SPECC1L,EP300,
HERC1,LZTR1,MICAL3,MKL1,MTMR3,MYH9,PI4KA,
RAPGEF1,SSH2,SUN2,TFIP11,TNRC6B,VPS13D,ZNF70
ATP9A,BTBD9,CCDC93,DGCR2,FOXJ3,FOXO3,FOXO3B,
IGF2R,INSR,KDM4B,KHNYN,MAGI1,MAML3,MICAL3,
MTMR3,PDPK1,SRGAP1,TLE3,TOM1L2,USP19,ZNF687
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 MTMR3


There's no related Drug.
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Cross referenced IDs for MTMR3
* 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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