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 MCCC1
Basic gene info.Gene symbolMCCC1
Gene namemethylcrotonoyl-CoA carboxylase 1 (alpha)
SynonymsMCC-B|MCCA
CytomapUCSC genome browser: 3q27
Genomic locationchr3 :182733005-182817365
Type of geneprotein-coding
RefGenesNM_001293273.1,
NM_020166.4,NR_120639.1,NR_120640.1,
Ensembl idENSG00000078070
Description3-methylcrotonyl-CoA carboxylase 13-methylcrotonyl-CoA carboxylase biotin-containing subunit3-methylcrotonyl-CoA:carbon dioxide ligase subunit alphaMCCase subunit alphamethylcrotonoyl-CoA carboxylase subunit alpha, mitochondrialmethylcrotonoyl-Coenzy
Modification date20141211
dbXrefs MIM : 609010
HGNC : HGNC
Ensembl : ENSG00000078070
HPRD : 01951
Vega : OTTHUMG00000158355
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MCCC1
BioGPS: 56922
Gene Expression Atlas: ENSG00000078070
The Human Protein Atlas: ENSG00000078070
PathwayNCI Pathway Interaction Database: MCCC1
KEGG: MCCC1
REACTOME: MCCC1
ConsensusPathDB
Pathway Commons: MCCC1
MetabolismMetaCyc: MCCC1
HUMANCyc: MCCC1
RegulationEnsembl's Regulation: ENSG00000078070
miRBase: chr3 :182,733,005-182,817,365
TargetScan: NM_001293273
cisRED: ENSG00000078070
ContextiHOP: MCCC1
cancer metabolism search in PubMed: MCCC1
UCL Cancer Institute: MCCC1
Assigned class in ccmGDBC

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Phenotypic Information for MCCC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MCCC1
Familial Cancer Database: MCCC1
* 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_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: MCCC1
MedGen: MCCC1 (Human Medical Genetics with Condition)
ClinVar: MCCC1
PhenotypeMGI: MCCC1 (International Mouse Phenotyping Consortium)
PhenomicDB: MCCC1

Mutations for MCCC1
* 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
* 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
ovaryMCCC1chr3182781687182781707chr3194703983194704003
prostateMCCC1chr3182780219182782219chr13114214556114216556
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 MCCC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW379082CAMSAP211491200730147200776570MCCC11392083182733257182733326
AA505323MCCC113653182747496182747860PTPN143624461214598488214598572

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 # sample11      3 1      
GAIN (# sample)11      3 1      
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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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=73)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=3)
There's no deleted 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
chr3:182756825-182756825p.R456C4
chr3:182733336-182733336p.K690E4
chr3:182775159-182775159p.L271F4
chr3:182740299-182740299p.E592G4
chr3:182738007-182738007p.D630Y2
chr3:182756857-182756857p.Q445R2
chr3:182789054-182789054p.A195T2
chr3:182740231-182740232p.E615K2
chr3:182756918-182756918p.E425K2
chr3:182789077-182789077p.S187L2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample52 161 2 31 1081  56 9
# mutation72 131 2 31 1091  66 11
nonsynonymous SNV52 111 1 21 68   55 9
synonymous SNV2  2  1 1  411  11 2
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
chr3:182740299p.E475G,MCCC14
chr3:182759359p.R66H2
chr3:182810273p.R304R,MCCC12
chr3:182738013p.T568T,MCCC11
chr3:182763328p.M459I,MCCC11
chr3:182755018p.R292Q,MCCC11
chr3:182789019p.R137S,MCCC11
chr3:182790262p.M17I,MCCC11
chr3:182733324p.I561I,MCCC11
chr3:182740260p.Y457Y,MCCC11

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 MCCC1 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 MCCC1

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

B3GNT5,DNAJB11,ECE2,EIF4G1,FAM136A,FBXO45,GMPS,
HRASLS,MCCC1,PAK1IP1,PDE7A,PLCH1,PSMD2,PSME4,
RFC4,SENP5,TBCCD1,TEX10,WDR53,YEATS2,ZNF695
ACACA,ACSS3,BCKDHB,APMAP,RHOV___CHP1,CSPG5,CYB5A,
EYS,FCN2,HIBCH,IDH1,LDHD,LSS,MCCC1,
ME1,PCCA,PCCB,SCP2,SLC27A2,SLC43A1,SUOX

ACAD8,ACADSB,ALDH6A1,ATP5F1,ATPAF1,BDH1,DBT,
EIF2B5,GFM1,GIPC2,MCCC1,MFN1,MINA,MRPS22,
NGLY1,OPA1,PCCB,SUCLG2,TFDP2,TOMM70A,ZZZ3
ADAMDEC1,C21orf33,CDCA7,DCAF12,FERMT1,FOXA1,KREMEN1,
LRPPRC,MCCC1,MLYCD,MTIF2,NGLY1,NUDT16P1,NUDT6,
QARS,RPIA,STARD7,SUCLG2,THNSL1,UNG,ZCCHC8
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 MCCC1
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
DB00121methylcrotonoyl-CoA carboxylase 1 (alpha)approved; nutraceuticalBiotin
DB00149methylcrotonoyl-CoA carboxylase 1 (alpha)approved; nutraceuticalL-Leucine


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Cross referenced IDs for MCCC1
* 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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