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 MTM1
Basic gene info.Gene symbolMTM1
Gene namemyotubularin 1
SynonymsCNM|MTMX|XLMTM
CytomapUCSC genome browser: Xq28
Genomic locationchrX :149737046-149841616
Type of geneprotein-coding
RefGenesNM_000252.2,
Ensembl idENSG00000269031
Descriptionmyotubularinphosphatidylinositol-3,5-bisphosphate 3-phosphatasephosphatidylinositol-3-phosphate phosphatase
Modification date20141219
dbXrefs MIM : 300415
HGNC : HGNC
Ensembl : ENSG00000171100
HPRD : 02331
Vega : OTTHUMG00000024158
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MTM1
BioGPS: 4534
Gene Expression Atlas: ENSG00000269031
The Human Protein Atlas: ENSG00000269031
PathwayNCI Pathway Interaction Database: MTM1
KEGG: MTM1
REACTOME: MTM1
ConsensusPathDB
Pathway Commons: MTM1
MetabolismMetaCyc: MTM1
HUMANCyc: MTM1
RegulationEnsembl's Regulation: ENSG00000269031
miRBase: chrX :149,737,046-149,841,616
TargetScan: NM_000252
cisRED: ENSG00000269031
ContextiHOP: MTM1
cancer metabolism search in PubMed: MTM1
UCL Cancer Institute: MTM1
Assigned class in ccmGDBC

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Phenotypic Information for MTM1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MTM1
Familial Cancer Database: MTM1
* 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: MTM1
MedGen: MTM1 (Human Medical Genetics with Condition)
ClinVar: MTM1
PhenotypeMGI: MTM1 (International Mouse Phenotyping Consortium)
PhenomicDB: MTM1

Mutations for MTM1
* 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 MTM1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AU125262MTM1174X149840337149840410EMG1737811270902467125842
AA506682MTM18212X149841153149841357MTM1208285X149841310149841387

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=80)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
There's no inserted snv.

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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
chr23:149809883-149809883p.R224*3
chr23:149814235-149814235p.R253Q3
chr23:149831928-149831928p.S497Y2
chr23:149807437-149807437p.E156K2
chr23:149814343-149814343p.K289T2
chr23:149767149-149767149p.T77M2
chr23:149809889-149809889p.P226S2
chr23:149814211-149814211p.P245R2
chr23:149828946-149828946p.R486*2
chr23:149787524-149787524p.L119P1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample37 82  1   721  61112
# mutation37 82  1   721  61113
nonsynonymous SNV37 72  1   621  61112
synonymous SNV   1       1       1
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
chrX:149814235p.R253Q3
chrX:149809819p.E156K2
chrX:149809889p.L202F2
chrX:149807437p.T77M2
chrX:149767149p.P226S2
chrX:149839986p.L144P1
chrX:149814303p.S272Y1
chrX:149787533p.W534L1
chrX:149831928p.I276V1
chrX:149809827p.I539V1

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 MTM1 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 MTM1

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

APOOL,BIRC6,C9orf41,CAB39,CUL4B,DDX3X,FAM199X,
FMR1,KDM6A,LOC284441,MAP3K2,MMGT1,MOB1A,MTM1,
MTMR1,PIKFYVE,STAG2,USP9X,VAMP7,WDR44,XIAP
ABHD13,ACBD3,ATF1,BIRC2,TRAPPC13,MAGT1,MARCH7,
MFN1,MTM1,MTMR6,MYNN,NAPG,NEDD1,STXBP3,
TBK1,TWISTNB,UBXN4,UTP15,VEZF1,YTHDC2,ZNF800

APOOL,ATP7A,BRWD3,CHM,CUL4B,CXorf56,ELF4,
FAM199X,GNL3L,HERC3,MMGT1,MTM1,MTMR1,OCRL,
RPS6KA6,SNX12,STAG2,UBQLN2,XIAP,YIPF6,ZNF41
ACVR1B,BCAS1,CAPN5,CLMN,EIF2AK3,ENDOD1,FGFR3,
GALNT12,IRF6,ITM2C,MCTP2,MTM1,NR3C2,PARM1,
PSD3,SCNN1A,SLC4A4,SPIRE2,STYK1,SYTL2,TMEM63B
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 MTM1


There's no related Drug.
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Cross referenced IDs for MTM1
* 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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