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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for ME3 |
Basic gene info. | Gene symbol | ME3 |
Gene name | malic enzyme 3, NADP(+)-dependent, mitochondrial | |
Synonyms | NADP-ME | |
Cytomap | UCSC genome browser: 11cen-q22.3 | |
Genomic location | chr11 :86152149-86383240 | |
Type of gene | protein-coding | |
RefGenes | NM_001014811.1, NM_006680.2,NM_001161586.1, | |
Ensembl id | ENSG00000151376 | |
Description | NADP-dependent malic enzyme, mitochondrialmalate dehydrogenasemalic enzyme, NADP+-dependent, mitochondrialmitochondrial NADP(+)-dependent malic enzyme 3pyruvic-malic carboxylase | |
Modification date | 20141207 | |
dbXrefs | MIM : 604626 | |
HGNC : HGNC | ||
Ensembl : ENSG00000151376 | ||
HPRD : 06862 | ||
Vega : OTTHUMG00000167217 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_ME3 | |
BioGPS: 10873 | ||
Gene Expression Atlas: ENSG00000151376 | ||
The Human Protein Atlas: ENSG00000151376 | ||
Pathway | NCI Pathway Interaction Database: ME3 | |
KEGG: ME3 | ||
REACTOME: ME3 | ||
ConsensusPathDB | ||
Pathway Commons: ME3 | ||
Metabolism | MetaCyc: ME3 | |
HUMANCyc: ME3 | ||
Regulation | Ensembl's Regulation: ENSG00000151376 | |
miRBase: chr11 :86,152,149-86,383,240 | ||
TargetScan: NM_001014811 | ||
cisRED: ENSG00000151376 | ||
Context | iHOP: ME3 | |
cancer metabolism search in PubMed: ME3 | ||
UCL Cancer Institute: ME3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for ME3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: ME3 |
Familial Cancer Database: ME3 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_PYRUVATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: ME3 |
MedGen: ME3 (Human Medical Genetics with Condition) | |
ClinVar: ME3 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
- Statistics for Tissue and Mutation type | Top |
- 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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | ME3 | chr11 | 86186130 | 86186150 | ME3 | chr11 | 86186068 | 86186088 |
ovary | ME3 | chr11 | 86194021 | 86194041 | DLG2 | chr11 | 84905243 | 84905263 |
ovary | ME3 | chr11 | 86211809 | 86211829 | chr11 | 86151691 | 86151711 | |
ovary | ME3 | chr11 | 86287124 | 86287144 | KTN1 | chr14 | 56079047 | 56079067 |
ovary | ME3 | chr11 | 86288751 | 86288771 | ME3 | chr11 | 86289166 | 86289186 |
ovary | ME3 | chr11 | 86335644 | 86335664 | ME3 | chr11 | 86315094 | 86315114 |
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) |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ME3 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
DA168920 | RPA3 | 26 | 246 | 7 | 7712936 | 7841375 | ME3 | 244 | 582 | 11 | 86219857 | 86270867 | |
BF760370 | TRIM52 | 21 | 317 | 5 | 180683957 | 180684253 | ME3 | 303 | 431 | 11 | 86183556 | 86183685 | |
BE844054 | ME3 | 21 | 201 | 11 | 86230131 | 86230311 | TPT1 | 202 | 329 | 13 | 45911455 | 45912853 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample | 3 | 1 |   | 1 |   |   | 1 |   | 2 |   | 2 |   |   | 2 | 4 |   |   | |||
GAIN (# sample) | 3 | 1 |   | 1 |   |   |   |   | 1 |   | 2 |   |   | 2 | 3 |   |   | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=50) | (# total SNVs=20) |
(# total SNVs=0) | (# total SNVs=0) |
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Top 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 position | Mutation(aa) | Unique sampleID count |
chr11:86152477-86152477 | p.L553L | 3 |
chr11:86158109-86158109 | p.E460K | 2 |
chr11:86209078-86209078 | p.L211Q | 2 |
chr11:86267657-86267657 | p.I135I | 2 |
chr11:86176191-86176191 | p.A287A | 1 |
chr11:86267677-86267677 | p.V129L | 1 |
chr11:86157450-86157450 | p.G487E | 1 |
chr11:86209017-86209017 | p.G231G | 1 |
chr11:86382866-86382866 | p.A41T | 1 |
chr11:86158197-86158197 | p.A430A | 1 |
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SNV Counts per Each Loci in TCGA data |
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Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 1 | 2 |   | 13 |   |   | 5 |   | 1 |   |   | 4 | 3 | 3 |   |   | 14 | 6 |   | 12 |
# mutation | 1 | 2 |   | 12 |   |   | 5 |   | 1 |   |   | 4 | 3 | 3 |   |   | 15 | 6 |   | 16 |
nonsynonymous SNV | 1 | 2 |   | 7 |   |   | 5 |   | 1 |   |   | 4 | 2 | 2 |   |   | 11 | 4 |   | 11 |
synonymous SNV |   |   |   | 5 |   |   |   |   |   |   |   |   | 1 | 1 |   |   | 4 | 2 |   | 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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Top 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 Position | Mutation(aa) | Unique sampleID count |
chr11:86152477 | p.L553L,ME3 | 3 |
chr11:86267657 | p.E460K,ME3 | 2 |
chr11:86158109 | p.I135I,ME3 | 2 |
chr11:86267641 | p.S371C,ME3 | 1 |
chr11:86158194 | p.V251M,ME3 | 1 |
chr11:86270833 | p.R99Q,ME3 | 1 |
chr11:86160993 | p.G487R,ME3 | 1 |
chr11:86198431 | p.R364K,ME3 | 1 |
chr11:86157429 | p.G231G,ME3 | 1 |
chr11:86267648 | p.L78P,ME3 | 1 |
Other DBs for Point Mutations |
Copy 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 |
Gene 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. |
Differential 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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for ME3 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | malic enzyme 3, NADP(+)-dependent, mitochondrial | approved; nutraceutical | NADH | ||
DB01907 | malic enzyme 3, NADP(+)-dependent, mitochondrial | experimental | Nicotinamide-Adenine-Dinucleotide | ||
DB03680 | malic enzyme 3, NADP(+)-dependent, mitochondrial | experimental | Tartronate | ||
DB00184 | malic enzyme 3, NADP(+)-dependent, mitochondrial | approved | Nicotine |
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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 |
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