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 MUT
Basic gene info.Gene symbolMUT
Gene namemethylmalonyl CoA mutase
SynonymsMCM
CytomapUCSC genome browser: 6p12.3
Genomic locationchr6 :49398072-49431041
Type of geneprotein-coding
RefGenesNM_000255.3,
Ensembl idENSG00000146085
Descriptionmethylmalonyl Coenzyme A mutasemethylmalonyl-CoA isomerasemethylmalonyl-CoA mutase, mitochondrial
Modification date20141219
dbXrefs MIM : 609058
HGNC : HGNC
Ensembl : ENSG00000146085
HPRD : 02014
Vega : OTTHUMG00000014814
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MUT
BioGPS: 4594
Gene Expression Atlas: ENSG00000146085
The Human Protein Atlas: ENSG00000146085
PathwayNCI Pathway Interaction Database: MUT
KEGG: MUT
REACTOME: MUT
ConsensusPathDB
Pathway Commons: MUT
MetabolismMetaCyc: MUT
HUMANCyc: MUT
RegulationEnsembl's Regulation: ENSG00000146085
miRBase: chr6 :49,398,072-49,431,041
TargetScan: NM_000255
cisRED: ENSG00000146085
ContextiHOP: MUT
cancer metabolism search in PubMed: MUT
UCL Cancer Institute: MUT
Assigned class in ccmGDBC

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

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

Mutations for MUT
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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 MUT related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=70)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr6:49419405-49419405p.R369P4
chr6:49409561-49409561p.A600A2
chr6:49419255-49419255p.P419L2
chr6:49426979-49426979p.I67M2
chr6:49419303-49419303p.R403Q2
chr6:49419381-49419381p.A377E2
chr6:49427098-49427098p.I28V2
chr6:49416630-49416630p.E448G2
chr6:49403260-49403260p.H678R2
chr6:49409556-49409556p.K602R2

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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
# sample13 41 1 1  1142  76 10
# mutation13 41 1 1  1342  77 10
nonsynonymous SNV13 41 1 1  74   64 9
synonymous SNV           6 2  13 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
chr6:49419405p.R369H2
chr6:49416531p.C533Y1
chr6:49399535p.A45T1
chr6:49426796p.N720S1
chr6:49408038p.R525M1
chr6:49416546p.L358R1
chr6:49421308p.H14Y1
chr6:49399567p.D709E1
chr6:49426879p.K519N1
chr6:49409663p.L345V1

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 MUT 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 MUT

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

ANGPTL5,CAPN11,CD2AP,CDC5L,CENPQ,CYP39A1,ENPP4,
GMCL1,GPR111,HSP90AB1,KCTD20,GLTSCR1L,LOC285501,MRPS10,
MUT,PFKFB2,POLH,PPP2R5D,SLC29A1,UBR2,ZNF318
ACBD5,ALDH6A1,TMEM245,CS,DBT,DHTKD1,IARS2,
KIAA1715,MPDZ,MPHOSPH9,MTMR10,MUT,NR3C1,OSBPL1A,
OXCT1,OXR1,PDP2,SUCLG2,TEAD1,TFDP2,TMLHE

ALDH6A1,CDC5L,CPT2,DBT,ENPP4,ENTPD5,FPGT,
GABPA,GMFB,GPBP1L1,MED23,MUT,BLOC1S5,NCOA4,
NDUFS1,PDCD4,SLC25A24,SLC35A3,SLC35A5,SUCLG2,UEVLD
AFG3L2,CASK,CCDC47,DTX4,EPB41L4B,GUF1,IMMT,
IQGAP2,KIAA1522,LACE1,LOC407835,MFSD9,MUT,MYO1D,
NCKAP5,PFKL,PTPRK,SGPP2,SH3RF1,SLC35F2,TMEM164
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 MUT
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00115methylmalonyl CoA mutaseapproved; nutraceuticalCyanocobalamin
DB00200methylmalonyl CoA mutaseapprovedHydroxocobalamin
DB00121methylmalonyl CoA mutaseapproved; nutraceuticalBiotin


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Cross referenced IDs for MUT
* 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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