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 ME2
Basic gene info.Gene symbolME2
Gene namemalic enzyme 2, NAD(+)-dependent, mitochondrial
SynonymsODS1
CytomapUCSC genome browser: 18q21
Genomic locationchr18 :48405431-48476162
Type of geneprotein-coding
RefGenesNM_001168335.1,
NM_002396.4,
Ensembl idENSG00000082212
DescriptionNAD-MENAD-dependent malic enzyme, mitochondrialmalate dehydrogenasepyruvic-malic carboxylase
Modification date20141207
dbXrefs MIM : 154270
HGNC : HGNC
HPRD : 01103
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ME2
BioGPS: 4200
Gene Expression Atlas: ENSG00000082212
The Human Protein Atlas: ENSG00000082212
PathwayNCI Pathway Interaction Database: ME2
KEGG: ME2
REACTOME: ME2
ConsensusPathDB
Pathway Commons: ME2
MetabolismMetaCyc: ME2
HUMANCyc: ME2
RegulationEnsembl's Regulation: ENSG00000082212
miRBase: chr18 :48,405,431-48,476,162
TargetScan: NM_001168335
cisRED: ENSG00000082212
ContextiHOP: ME2
cancer metabolism search in PubMed: ME2
UCL Cancer Institute: ME2
Assigned class in ccmGDBC

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Phenotypic Information for ME2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ME2
Familial Cancer Database: ME2
* 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_PYRUVATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ME2
MedGen: ME2 (Human Medical Genetics with Condition)
ClinVar: ME2
PhenotypeMGI: ME2 (International Mouse Phenotyping Consortium)
PhenomicDB: ME2

Mutations for ME2
* 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
ovaryME2chr184845934348459363DPP10chr2116168412116168432
pancreasME2chr184842310548423125chr184875381148753831
pancreasME2chr184845069348450713chr184861496748614987
pancreasME2chr184845790048457920chr184867148548671505
pancreasME2chr184846143448461454chr184881533348815353
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 ME2 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 # sample1     4 1     1  
GAIN (# sample)        1        
LOSS (# sample)1     4       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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=15)
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
chr18:48458685-48458685p.R458*3
chr18:48473521-48473521p.E574E3
chr18:48446853-48446853p.F254F3
chr18:48439207-48439207p.E93D2
chr18:48439240-48439240p.I104M2
chr18:48444557-48444557p.D236D2
chr18:48434431-48434431p.?2
chr18:48434439-48434439p.A39T2
chr18:48442553-48442553p.S136S2
chr18:48439180-48439180p.Y84Y1

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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
# sample 2 101 2 21 73   44 8
# mutation 2 91 2 21 103   44 11
nonsynonymous SNV 2 71 1 21 92   13 9
synonymous SNV   2  1    11   31 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
chr18:48422269p.E93D,ME22
chr18:48434439p.P27S,ME22
chr18:48439207p.A39T,ME22
chr18:48439249p.Y84Y,ME21
chr18:48473422p.A293V,ME21
chr18:48447032p.Q509K1
chr18:48422209p.R91T,ME21
chr18:48452221p.I298I,ME21
chr18:48439273p.A527S1
chr18:48473427p.E329Q,ME21

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 ME2 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 ME2

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

MB21D1,CENPA,DSC2,ELAC1,AMER1,FAM171A1,FOXM1,
GPR63,MALT1,ME2,MEX3C,NARS,PUS7,R3HDM1,
RAD51AP1,SKA1,SRPK1,SUV39H2,TAF4B,TEX10,WDR43
AP1S2,BTBD1,TCAIM,CAB39,CAMK2D,CAPZA2,EGLN1,
GTPBP8,KPNA3,KPNA4,LOC653653,ME2,MEMO1,NAA50,
OSBPL11,PLCL2,PPP3CB,RRAGD,SLC16A1,TM6SF1,TTL

ATP5A1,ATP5B,ATPAF2,TIMM21,C1QBP,CHAC2,CNDP2,
DLST,EIF4A1,ELAC1,FECH,IER3IP1,KIAA1468,MBD2,
ME2,NARS,PCCB,PIAS2,SCO1,SKA1,TXNL1
ABCD3,ABHD5,AKR1B10,DECR1,ECHS1,MICU2,ETFA,
ETFDH,ETNK1,FAM107B,FAM45A,FDX1,GCLM,GHITM,
ME2,MTCH2,NRAS,PITX2,SLMO2,TGFA,UGDH
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 ME2
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
DB00157malic enzyme 2, NAD(+)-dependent, mitochondrialapproved; nutraceuticalNADH
DB01677malic enzyme 2, NAD(+)-dependent, mitochondrialexperimentalFumarate
DB01907malic enzyme 2, NAD(+)-dependent, mitochondrialexperimentalNicotinamide-Adenine-Dinucleotide
DB03499malic enzyme 2, NAD(+)-dependent, mitochondrialexperimentalMalate Ion
DB03589malic enzyme 2, NAD(+)-dependent, mitochondrialexperimentalAlpha-Ketomalonic Acid
DB03680malic enzyme 2, NAD(+)-dependent, mitochondrialexperimentalTartronate


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Cross referenced IDs for ME2
* 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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