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 MTMR1

Basic gene info.	Gene symbol	MTMR1
	Gene name	myotubularin related protein 1
	Synonyms	-
	Cytomap	UCSC genome browser: Xq28
	Genomic location	chrX :149861868-149933575
	Type of gene	protein-coding
	RefGenes	NM_003828.2, NM_176789.1,
	Ensembl id	ENSG00000269759
	Description	myotubularin-related protein 1phosphatidylinositol-3-phosphate phosphatase
	Modification date	20141207
dbXrefs	MIM : 300171
	HGNC : HGNC
	Ensembl : ENSG00000063601
	HPRD : 02163
	Vega : OTTHUMG00000024159
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MTMR1
	BioGPS: 8776
	Gene Expression Atlas: ENSG00000269759
	The Human Protein Atlas: ENSG00000269759
Pathway	NCI Pathway Interaction Database: MTMR1
	KEGG: MTMR1
	REACTOME: MTMR1
	ConsensusPathDB
	Pathway Commons: MTMR1
Metabolism	MetaCyc: MTMR1
	HUMANCyc: MTMR1
Regulation	Ensembl's Regulation: ENSG00000269759
	miRBase: chrX :149,861,868-149,933,575
	TargetScan: NM_003828
	cisRED: ENSG00000269759
Context	iHOP: MTMR1
	cancer metabolism search in PubMed: MTMR1
	UCL Cancer Institute: MTMR1
Assigned class in ccmGDB	C

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Phenotypic Information for MTMR1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: MTMR1
	Familial Cancer Database: MTMR1

* 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_RIBOFLAVIN_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_PI_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MTMR1
	MedGen: MTMR1 (Human Medical Genetics with Condition)
	ClinVar: MTMR1
Phenotype	MGI: MTMR1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: MTMR1

Mutations for MTMR1

* 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 MTMR1 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
M78377	DYRK1A	1	106	21	38809313	38809418	MTMR1	107	342	X	149895693	149898617
BF365519	ZC3HC1	19	213	7	129677558	129677752	MTMR1	204	321	X	149880963	149881080
BF365539	MTMR1	5	105	X	149880963	149881065	ZC3HC1	96	295	7	129677553	129677752
DB343893	LASP1	1	118	17	37077904	37078021	MTMR1	113	543	X	149931373	149931802

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=58)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=2)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

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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
chr23:149901048-149901048	p.T301M	4
chr23:149924177-149924177	p.T558M	3
chr23:149931175-149931175	p.S657S	2
chr23:149912872-149912872	p.R497*	2
chr23:149905142-149905142	p.H378Y	2
chr23:149867658-149867658	p.?	2
chr23:149905164-149905164	p.R385H	2
chr23:149931081-149931081	p.A626V	2
chr23:149896165-149896165	p.F145V	2
chr23:149901147-149901147	p.S334*	2

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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=4

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	1	1	13	3				2			4		2			3	2	1	10
# mutation	2	1	1	11	3				2			6		2			3	2	1	14
nonsynonymous SNV	2	1	1	6	2				2			5		2			3	2		11
synonymous SNV				5	1							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
chrX:149901048	p.T301M	4
chrX:149931091	p.S657S	2
chrX:149931175	p.T558M	2
chrX:149924177	p.F145V	2
chrX:149896165	p.Q629Q	2
chrX:149924281	p.F257L	1
chrX:149898617	p.E428Q	1
chrX:149901131	p.D273A	1
chrX:149905819	p.S450T	1
chrX:149931076	p.D274N	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 MTMR1 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 MTMR1

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


ARPC4,ATG7,BRPF1,BRK1,TAMM41,CIDECP,FANCD2, IL17RC,JAGN1,LOC401052,LSM3,MRPS25,MTMR14,OGG1, RPUSD3,SEC13,SSNA1,TADA3,TATDN2,EMC3,ZDHHC12	ANAPC11,AUP1,C19orf53,CHKB,IDH3G,MIIP,MPND, MTMR14,NAGPA,OAZ1,PLEKHO1,PNKD,POLD4,SLC2A8, TAZ,TPRA1,URM1,VPS28,WDR13,WDR45,ZMAT5

ARPC4,CCDC12,CIDECP,GORASP1,HDAC11,HEMK1,IL17RE, IP6K2,JAGN1,LRRFIP2,MTMR14,MYD88,OXSR1,PRKCD, RAF1,SHISA5,SLC25A38,TADA3,EMC3,TMEM115,TWF2	ACADS,KDF1,CBLC,CYB561A3,GMIP,GPN2,GRK6, GTF3C5,LLGL2,MPND,MTMR14,PFKL,PRRG2,SDC1, SH2D3A,SHKBP1,SIGIRR,STAP2,TBC1D22A,TOR2A,ZDHHC12

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 MTMR1

There's no related Drug.

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Cross referenced IDs for MTMR1

* 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