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 ME1
Basic gene info.Gene symbolME1
Gene namemalic enzyme 1, NADP(+)-dependent, cytosolic
SynonymsHUMNDME|MES
CytomapUCSC genome browser: 6q12
Genomic locationchr6 :83920109-84140938
Type of geneprotein-coding
RefGenesNM_002395.5,
Ensembl idENSG00000065833
DescriptionMalic enzyme, cytoplasmicNADP-MENADP-dependent malic enzymemalate dehydrogenasemalic enzyme 1, solublepyruvic-malic carboxylase
Modification date20141207
dbXrefs MIM : 154250
HGNC : HGNC
Ensembl : ENSG00000065833
HPRD : 01102
Vega : OTTHUMG00000015111
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ME1
BioGPS: 4199
Gene Expression Atlas: ENSG00000065833
The Human Protein Atlas: ENSG00000065833
PathwayNCI Pathway Interaction Database: ME1
KEGG: ME1
REACTOME: ME1
ConsensusPathDB
Pathway Commons: ME1
MetabolismMetaCyc: ME1
HUMANCyc: ME1
RegulationEnsembl's Regulation: ENSG00000065833
miRBase: chr6 :83,920,109-84,140,938
TargetScan: NM_002395
cisRED: ENSG00000065833
ContextiHOP: ME1
cancer metabolism search in PubMed: ME1
UCL Cancer Institute: ME1
Assigned class in ccmGDBC

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Phenotypic Information for ME1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ME1
Familial Cancer Database: ME1
* 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
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ME1
MedGen: ME1 (Human Medical Genetics with Condition)
ClinVar: ME1
PhenotypeMGI: ME1 (International Mouse Phenotyping Consortium)
PhenomicDB: ME1

Mutations for ME1
* 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
pancreasME1chr68392399883924018ME1chr68392406483924084
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 ME1 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 # sample2                
GAIN (# sample)2                
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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=53)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr6:84117513-84117513p.F62F5
chr6:83921695-83921695p.C556Y3
chr6:83921764-83921764p.P533L3
chr6:83926249-83926249p.I506F2
chr6:83947499-83947499p.G321G2
chr6:84056027-84056027p.R155R2
chr6:83938569-83938569p.E370*2
chr6:84117596-84117596p.R35G2
chr6:84025054-84025054p.E227K2
chr6:83937058-83937058p.T424I2

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  122 1 1  323  253 12
# mutation2  142 1 1  323  243 15
nonsynonymous SNV2  121 1 1  212  182 13
synonymous SNV   21      111  61 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
chr6:84117513p.F62F5
chr6:83921771p.E83K2
chr6:83937058p.T424I2
chr6:84108201p.P531S2
chr6:84025057p.R344C1
chr6:83921765p.D223N1
chr6:84056027p.S92C1
chr6:83933648p.K525N1
chr6:83949287p.P323S1
chr6:84108219p.D222N1

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 ME1 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 ME1

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

ACSL1,ACSM3,AKR1B15,EYS,FANCB,FUCA2,G6PD,
GJA10,HCCS,IDI1,KPNA7,LOC255167,ME1,OR9K2,
PGM3,PIGA,PIR,PSMD14,SRD5A1,VSX2,WDR64
ABCC6,ACACA,ACADL,ACSL1,ACSS2,ANO3,CDH20,
CPA2,CYB5A,EYS,FADS1,GCLC,HIBCH,IDH1,
LSS,MCCC1,ME1,PNPLA3,SUOX,THRSP,TSKU

ABHD3,AKR1B10,GSKIP,CYSTM1,RHOV___CHP1,KCNK1,LGALS3,
LGR4,LRRC1,ME1,PRSS12,RIOK3,SERPINB5,SH3BGRL3,
SLC17A5,SLC1A1,STYK1,TMEM92,TPMT,TSPAN13,VAPA
C6orf223,CEACAM4,CHRNA5,CLEC4E,CTPS1,EPHA6,FER,
FREM2,JAKMIP2,LOC100302640,ME1,NXNL1,TENM2,P4HA3,
RSPO2,S100A11,SNORA47,ST7,SYT12,UPF3B,WBP4
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 ME1
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 1, NADP(+)-dependent, cytosolicapproved; nutraceuticalNADH
DB03461malic enzyme 1, NADP(+)-dependent, cytosolicexperimental2'-Monophosphoadenosine 5'-Diphosphoribose


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Cross referenced IDs for ME1
* 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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