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 MTMR3

Basic gene info.	Gene symbol	MTMR3
	Gene name	myotubularin related protein 3
	Synonyms	FYVE-DSP1\|ZFYVE10
	Cytomap	UCSC genome browser: 22q12.2
	Genomic location	chr22 :30279157-30426857
	Type of gene	protein-coding
	RefGenes	NM_021090.3, NM_153050.2,NM_153051.2,NM_001013676.1,
	Ensembl id	ENSG00000100330
	Description	FYVE (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 date	20141207
dbXrefs	MIM : 603558
	HGNC : HGNC
	Ensembl : ENSG00000100330
	HPRD : 09151
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTMR3
	BioGPS: 8897
	Gene Expression Atlas: ENSG00000100330
	The Human Protein Atlas: ENSG00000100330
Pathway	NCI Pathway Interaction Database: MTMR3
	KEGG: MTMR3
	REACTOME: MTMR3
	ConsensusPathDB
	Pathway Commons: MTMR3
Metabolism	MetaCyc: MTMR3
	HUMANCyc: MTMR3
Regulation	Ensembl's Regulation: ENSG00000100330
	miRBase: chr22 :30,279,157-30,426,857
	TargetScan: NM_021090
	cisRED: ENSG00000100330
Context	iHOP: MTMR3
	cancer metabolism search in PubMed: MTMR3
	UCL Cancer Institute: MTMR3
Assigned class in ccmGDB	C

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Phenotypic Information for MTMR3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MTMR3
	MedGen: MTMR3 (Human Medical Genetics with Condition)
	ClinVar: MTMR3
Phenotype	MGI: MTMR3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	MTMR3	chr22	30374137	30374157	MTMR3	chr22	30370943	30370963
pancreas	MTMR3	chr22	30287505	30287705		chr22	35999595	35999795
pancreas	MTMR3	chr22	30301243	30301263	NF2	chr22	30058981	30059001
pancreas	MTMR3	chr22	30335572	30335592	NEFH	chr22	29879547	29879567

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MTMR3 related fusion information.

ID	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
BG469920	MTMR3	2	124	22	30279226	30279348	APOH	124	873	17	64212981	64225541
BG824141	MTMR3	2	178	22	30279172	30279348	APOH	178	827	17	64216676	64225541
BE764648	LOC286467	15	95	X	130942349	130942428	MTMR3	88	262	22	30423444	30423618
T05096	MTMR3	1	105	22	30304242	30304346	BRWD1	105	373	21	40560343	40560610

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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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=1

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Somatic 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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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
chr22:30416328-30416329	p.Q894fs*8	2
chr22:30418071-30418071	p.C1093C	1
chr22:30409357-30409357	p.L444F	1
chr22:30421732-30421732	p.P1180L	1
chr22:30409438-30409438	p.E471K	1
chr22:30409486-30409486	p.Q487K	1
chr22:30412561-30412561	p.F516L	1
chr22:30413924-30413924	p.Y561Y	1
chr22:30416336-30416338	p.S897delS	1
chr22:30387596-30387596	p.H133Y	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	5	3		11	1		1		3	1	1	4	7	1			12	13	1	7
# mutation	5	3		12	1		1		3	1	1	6	7	1			14	13	1	9
nonsynonymous SNV	5	3		8	1				1		1	4	7				10	9	1	5
synonymous SNV				4			1		2	1		2		1			4	4		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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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
chr22:30416522	p.R671K,MTMR3	2
chr22:30415660	p.S208T,MTMR3	2
chr22:30398934	p.C958C,MTMR3	2
chr22:30403281	p.R1055H,MTMR3	1
chr22:30415931	p.A117T,MTMR3	1
chr22:30421762	p.R407W,MTMR3	1
chr22:30412561	p.T618N,MTMR3	1
chr22:30416424	p.R838G,MTMR3	1
chr22:30387543	p.L1085M	1
chr22:30415499	p.E164Q,MTMR3	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 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

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


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

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 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