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 ME3
Basic gene info.Gene symbolME3
Gene namemalic enzyme 3, NADP(+)-dependent, mitochondrial
SynonymsNADP-ME
CytomapUCSC genome browser: 11cen-q22.3
Genomic locationchr11 :86152149-86383240
Type of geneprotein-coding
RefGenesNM_001014811.1,
NM_006680.2,NM_001161586.1,
Ensembl idENSG00000151376
DescriptionNADP-dependent malic enzyme, mitochondrialmalate dehydrogenasemalic enzyme, NADP+-dependent, mitochondrialmitochondrial NADP(+)-dependent malic enzyme 3pyruvic-malic carboxylase
Modification date20141207
dbXrefs MIM : 604626
HGNC : HGNC
Ensembl : ENSG00000151376
HPRD : 06862
Vega : OTTHUMG00000167217
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ME3
BioGPS: 10873
Gene Expression Atlas: ENSG00000151376
The Human Protein Atlas: ENSG00000151376
PathwayNCI Pathway Interaction Database: ME3
KEGG: ME3
REACTOME: ME3
ConsensusPathDB
Pathway Commons: ME3
MetabolismMetaCyc: ME3
HUMANCyc: ME3
RegulationEnsembl's Regulation: ENSG00000151376
miRBase: chr11 :86,152,149-86,383,240
TargetScan: NM_001014811
cisRED: ENSG00000151376
ContextiHOP: ME3
cancer metabolism search in PubMed: ME3
UCL Cancer Institute: ME3
Assigned class in ccmGDBC

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Phenotypic Information for ME3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ME3
Familial Cancer Database: ME3
* 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: ME3
MedGen: ME3 (Human Medical Genetics with Condition)
ClinVar: ME3
PhenotypeMGI: ME3 (International Mouse Phenotyping Consortium)
PhenomicDB: ME3

Mutations for ME3
* 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
ovaryME3chr118618613086186150ME3chr118618606886186088
ovaryME3chr118619402186194041DLG2chr118490524384905263
ovaryME3chr118621180986211829chr118615169186151711
ovaryME3chr118628712486287144KTN1chr145607904756079067
ovaryME3chr118628875186288771ME3chr118628916686289186
ovaryME3chr118633564486335664ME3chr118631509486315114
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 ME3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA168920RPA326246777129367841375ME3244582118621985786270867
BF760370TRIM52213175180683957180684253ME3303431118618355686183685
BE844054ME321201118623013186230311TPT1202329134591145545912853

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 # sample31 1  1 2 2  24  
GAIN (# sample)31 1    1 2  23  
LOSS (# sample)      1 1     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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=50)
Stat. for Synonymous SNVs
(# total SNVs=20)
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
chr11:86152477-86152477p.L553L3
chr11:86158109-86158109p.E460K2
chr11:86209078-86209078p.L211Q2
chr11:86267657-86267657p.I135I2
chr11:86382865-86382865p.A41G1
chr11:86158143-86158143p.A448A1
chr11:86198484-86198484p.?1
chr11:86152479-86152479p.L553I1
chr11:86160976-86160976p.A362A1
chr11:86209141-86209141p.R190H1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 13  5 1  433  146 12
# mutation12 12  5 1  433  156 16
nonsynonymous SNV12 7  5 1  422  114 11
synonymous SNV   5        11  42 5
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
chr11:86152477p.L553L,ME33
chr11:86267657p.E460K,ME32
chr11:86158109p.I135I,ME32
chr11:86160981p.L78P,ME31
chr11:86270824p.E477K,ME31
chr11:86157399p.R364K,ME31
chr11:86198421p.G231G,ME31
chr11:86158194p.H76Q,ME31
chr11:86267641p.I464V,ME31
chr11:86160993p.A362A,ME31

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 ME3 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 ME3

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

C16orf86,CCDC24,CCNL2,CIRBP,CROCC,CROCCP3,HDAC7,
LOC115110,MAN2C1,ME3,MTMR9LP,MYO15B,MZF1,NEIL1,
NISCH,PGPEP1,PHF1,PRSS23,RBM5,TNFRSF14,UBXN11
ACAA2,PHYKPL,AIFM2,AOC3,AQP7,CALB2,CIDECP,
DOK1,GDPD5,GPD1,GPER1,KCNIP2,LIPE,ME3,
MGLL,PDXK,RDH5,TK2,TMEM140,TYRO3,VTI1B

AIFM3,ANKRD9,ASCL2,C10orf82,LINC00526,FHDC1,H2AFJ,
IP6K2,LIN7B,ME3,MTL5,NUDT14,OR6M1,PAAF1,
PRDX5,PRSS23,QTRT1,SETMAR,SLC37A4,VENTX,ZNF202
AGFG2,AP3S2,APOBEC3B,AQP8,CA2,CDK3,FABP1,
GLB1L2,HSD17B2,LANCL3,ME3,NRG4,PDE6A,PPP1R14C,
SFXN5,SGK2,SLC16A1,SLC20A1,SLC4A9,UGT1A10,UGT1A8
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 ME3
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 3, NADP(+)-dependent, mitochondrialapproved; nutraceuticalNADH
DB01907malic enzyme 3, NADP(+)-dependent, mitochondrialexperimentalNicotinamide-Adenine-Dinucleotide
DB03680malic enzyme 3, NADP(+)-dependent, mitochondrialexperimentalTartronate
DB00184malic enzyme 3, NADP(+)-dependent, mitochondrialapprovedNicotine


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Cross referenced IDs for ME3
* 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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