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 MMAB
Basic gene info.Gene symbolMMAB
Gene namemethylmalonic aciduria (cobalamin deficiency) cblB type
SynonymsATR|CFAP23|cblB|cob
CytomapUCSC genome browser: 12q24
Genomic locationchr12 :109991520-110011358
Type of geneprotein-coding
RefGenesNM_052845.3,
NR_038118.1,
Ensembl idENSG00000139428
DescriptionATP:cob(I)alamin adenosyltransferaseATP:corrinoid adenosyltransferaseaquocob(I)alamin vitamin B12s adenosyltransferasecilia and flagella associated protein 23cob(I)yrinic acid a,c-diamide adenosyltransferase, mitochondrialmethylmalonic aciduria type
Modification date20141219
dbXrefs MIM : 607568
HGNC : HGNC
Ensembl : ENSG00000139428
HPRD : 07398
Vega : OTTHUMG00000169255
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MMAB
BioGPS: 326625
Gene Expression Atlas: ENSG00000139428
The Human Protein Atlas: ENSG00000139428
PathwayNCI Pathway Interaction Database: MMAB
KEGG: MMAB
REACTOME: MMAB
ConsensusPathDB
Pathway Commons: MMAB
MetabolismMetaCyc: MMAB
HUMANCyc: MMAB
RegulationEnsembl's Regulation: ENSG00000139428
miRBase: chr12 :109,991,520-110,011,358
TargetScan: NM_052845
cisRED: ENSG00000139428
ContextiHOP: MMAB
cancer metabolism search in PubMed: MMAB
UCL Cancer Institute: MMAB
Assigned class in ccmGDBC

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

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

Mutations for MMAB
* 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
ovaryMMABchr12110005358110005378MMABchr12110001311110001331
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 MMAB 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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr12:110011229-110011229p.R19R3
chr12:110011230-110011230p.R19H3
chr12:110006627-110006627p.D80N3
chr12:109994930-109994930p.Y219C3
chr12:109998867-109998867p.V188M2
chr12:109994870-109994870p.M239K2
chr12:109999595-109999595p.E137E2
chr12:110009504-110009504p.S49F2
chr12:109998845-109998845p.R195H1
chr12:110002938-110002938p.E112K1

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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
# sample11131   1  2    22 2
# mutation11131   1  2    22 2
nonsynonymous SNV  131   1  2    21 2
synonymous SNV11               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
chr12:110002938p.E112K2
chr12:109998860p.R190H2
chr12:109998898p.C132S1
chr12:109999605p.K106K1
chr12:109999611p.E91K1
chr12:109994869p.G87E1
chr12:110002954p.R75S1
chr12:109994891p.S49Y1
chr12:110006594p.M239I1
chr12:109994906p.G232V1

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 MMAB 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 MMAB

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

COX14,UQCC2,DCXR,DHRS4,DHRS4L2,DPM2,EDF1,
ENDOG,LENG9,MMAB,MRPL28,MRPL41,MVK,PHPT1,
PSMD9,SDSL,SURF1,TIMM13,TMEM141,TMEM160,UFSP1
AACS,ACAT2,ACY1,BCAT2,URB1-AS1,DBI,DCXR,
DHCR7,EBP,FDPS,GSS,GSTZ1,HIST1H1C,HIST2H2AA3,
IVD,MMAB,MVD,MVK,NSDHL,PEX10,REEP6

ARL6IP4,CDK4,COX6A1,DIABLO,EBP,METTL1,MMAB,
MVK,NDUFA12,NOC4L,NUP37,NABP2,PA2G4,RAN,
RPLP0,SRSF9,SLC25A3,SNRPF,TARBP2,TSFM,TUBA1C
BOLA3,HYPK,EBNA1BP2,EIF3I,EIF5A,EIF5AL1,HSD17B7,
MMAB,MRPL17,MRPL20,MRPL52,NHP2,NME1,PPIL1,
PSMA7,PSMD14,RAN,RFC2,SNRPG,TMSB10,TOMM5
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 MMAB
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
DB00200methylmalonic aciduria (cobalamin deficiency) cblB typeapprovedHydroxocobalamin


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Cross referenced IDs for MMAB
* 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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