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 MCCC2
Basic gene info.Gene symbolMCCC2
Gene namemethylcrotonoyl-CoA carboxylase 2 (beta)
SynonymsMCCB
CytomapUCSC genome browser: 5q12-q13
Genomic locationchr5 :70883114-70954530
Type of geneprotein-coding
RefGenesNM_022132.4,
Ensembl idENSG00000262057
Description3-methylcrotonyl-CoA carboxylase 23-methylcrotonyl-CoA carboxylase non-biotin-containing subunit3-methylcrotonyl-CoA:carbon dioxide ligase subunit betaMCCase subunit betabiotin carboxylasemethylcrotonoyl-CoA carboxylase beta chain, mitochondrialmeth
Modification date20141207
dbXrefs MIM : 609014
HGNC : HGNC
Ensembl : ENSG00000131844
HPRD : 01952
Vega : OTTHUMG00000162505
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MCCC2
BioGPS: 64087
Gene Expression Atlas: ENSG00000262057
The Human Protein Atlas: ENSG00000262057
PathwayNCI Pathway Interaction Database: MCCC2
KEGG: MCCC2
REACTOME: MCCC2
ConsensusPathDB
Pathway Commons: MCCC2
MetabolismMetaCyc: MCCC2
HUMANCyc: MCCC2
RegulationEnsembl's Regulation: ENSG00000262057
miRBase: chr5 :70,883,114-70,954,530
TargetScan: NM_022132
cisRED: ENSG00000262057
ContextiHOP: MCCC2
cancer metabolism search in PubMed: MCCC2
UCL Cancer Institute: MCCC2
Assigned class in ccmGDBC

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Phenotypic Information for MCCC2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: MCCC2
Familial Cancer Database: MCCC2
* 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: MCCC2
MedGen: MCCC2 (Human Medical Genetics with Condition)
ClinVar: MCCC2
PhenotypeMGI: MCCC2 (International Mouse Phenotyping Consortium)
PhenomicDB: MCCC2

Mutations for MCCC2
* 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
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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryMCCC2chr57089059970890619chr57108306571083085
ovaryMCCC2chr57090875270908772ADAMTS6chr56458028164580301
ovaryMCCC2chr57093645870936478chr55824775658247776
prostateMCCC2chr57094164870941648chr57493757274937572
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 MCCC2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample      1   1      
GAIN (# sample)      1          
LOSS (# sample)          1      
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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=51)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
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
chr5:70927955-70927955p.A249V11
chr5:70939693-70939693p.G374R3
chr5:70952669-70952669p.F558F2
chr5:70900248-70900248p.R193S2
chr5:70946013-70946013p.?2
chr5:70948577-70948577p.A524T2
chr5:70944989-70944989p.A428T2
chr5:70952586-70952586p.I531F1
chr5:70922545-70922545p.K235*1
chr5:70939654-70939654p.R361*1

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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
# sample1  41 4 5  61   53 7
# mutation1  51 4 5  61   53 8
nonsynonymous SNV1  5  2 5  61   33 6
synonymous SNV    1 2         2  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
chr5:70927976p.R193S2
chr5:70944989p.A428T2
chr5:70900248p.S256F2
chr5:70931014p.D264G1
chr5:70948577p.A524T1
chr5:70892176p.N89S1
chr5:70922483p.H275D1
chr5:70931042p.D536H1
chr5:70952601p.T121A1
chr5:70895565p.H275Q1

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 MCCC2 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 MCCC2

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

AGGF1,ANKHD1-EIF4EBP3,ANKRA2,KIAA0825,CCDC125,DCTN4,FBXO38,
FOXA1,GIN1,MARVELD2,MCCC2,MRPS27,NUDT12,PGGT1B,
PTCD2,RAD50,REEP5,SKP1,SLC22A5,TMBIM6,YTHDC2
ACSL3,ALDH3B2,ALOX15B,ENPP3,GGT1,LONP2,MBOAT2,
MCCC2,MOGAT2,MPV17L,NANOG,NAT2,NSUN2,PON3,
SERHL,SPINK8,SRD5A1,TMEM45B,TMEM62,UGT2B10,UGT2B11

ACADSB,ALDH7A1,AP3B1,SMIM15,COX7C,CS,DLD,
GOT2,HNRNPAB,HSD17B4,HSPA9,LARS2,LARS,MARS2,
MCCC2,MRPS27,MRPS36,NLN,TAF9,TMEM161B,UTP15
ANKEF1,DARS2,DCAF12,FAM120A,FAM81A,HSPA9,IARS2,
LRPPRC,MCCC2,MECOM,MIPEP,MLEC,MTIF2,PDHA1,
PKP2,PPIP5K2,PROM2,RPIA,SRPK1,STARD7,UGT8
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 MCCC2
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 2 (beta)approved; nutraceuticalBiotin
DB00149methylcrotonoyl-CoA carboxylase 2 (beta)approved; nutraceuticalL-Leucine
DB01033methylcrotonoyl-CoA carboxylase 2 (beta)approvedMercaptopurine
DB00563methylcrotonoyl-CoA carboxylase 2 (beta)approvedMethotrexate


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Cross referenced IDs for MCCC2
* 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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