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 MLEC
Basic gene info.Gene symbolMLEC
Gene namemalectin
SynonymsKIAA0152
CytomapUCSC genome browser: 12q24.31
Genomic locationchr12 :121124948-121139667
Type of geneprotein-coding
RefGenesNM_014730.2,
Ensembl idENSG00000110917
Descriptionoligosaccharyltransferase complex subunit (non-catalytic)
Modification date20141207
dbXrefs MIM : 613802
HGNC : HGNC
Ensembl : ENSG00000110917
HPRD : 13781
Vega : OTTHUMG00000169187
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MLEC
BioGPS: 9761
Gene Expression Atlas: ENSG00000110917
The Human Protein Atlas: ENSG00000110917
PathwayNCI Pathway Interaction Database: MLEC
KEGG: MLEC
REACTOME: MLEC
ConsensusPathDB
Pathway Commons: MLEC
MetabolismMetaCyc: MLEC
HUMANCyc: MLEC
RegulationEnsembl's Regulation: ENSG00000110917
miRBase: chr12 :121,124,948-121,139,667
TargetScan: NM_014730
cisRED: ENSG00000110917
ContextiHOP: MLEC
cancer metabolism search in PubMed: MLEC
UCL Cancer Institute: MLEC
Assigned class in ccmGDBC

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

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

Mutations for MLEC
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MLEC related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI632281TERF116187395860573958665MLEC5238612121135317121135651
BE550278TERF116187395860573958665MLEC5238512121135317121135651
AI656269TERF116187395860573958665MLEC5238512121135317121135651
AI962170TERF116187395860573958665MLEC5238612121135317121135651
BE501371TERF116187395860573958665MLEC5238512121135317121135651
BG955818MUC5B112101112713301271533MLEC20240312121139214121139415
AI825089TERF116187395860573958665MLEC5229012121135412121135651
AA243990MLEC815812121139379121139529MLEC15745012121139070121139364
BF806090MLEC829212121125681121125966MAGI128755336572024465720510
AA244053MLEC138312121138982121139364MLEC38249312121139418121139529
BE930957MOB3B3513692739337627393478MLEC12947012121134483121134823
AI651406TXNDC9135129995394599977642MLEC34637412121137167121137195

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 # sample              1  
GAIN (# sample)              1  
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=28)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=2)
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
chr12:121132050-121132050p.Y131C2
chr12:121134166-121134168p.E233delE2
chr12:121134168-121134168p.E233E2
chr12:121132708-121132708p.D166N2
chr12:121134118-121134118p.?1
chr12:121132798-121132798p.V196F1
chr12:121134138-121134138p.P223P1
chr12:121132062-121132062p.S135Y1
chr12:121132899-121132899p.G198V1
chr12:121134143-121134143p.P225L1

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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
# sample21 8  1 1  631 112 3
# mutation21 8  1 1  631 112 3
nonsynonymous SNV11 6  1 1  521 111 2
synonymous SNV1  2       11    1 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
chr12:121132708p.D166N2
chr12:121131987p.K177T1
chr12:121132908p.E183K1
chr12:121132062p.V36M1
chr12:121132930p.V196F1
chr12:121125205p.G198V1
chr12:121132064p.A51A1
chr12:121134125p.Y200H1
chr12:121125252p.R78L1
chr12:121132627p.Y200Y1

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 MLEC 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 MLEC

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

ALDH6A1,ANKRD52,ARL1,BAZ2A,CCNT1,CMTM4,CYB561D1,
FICD,GCN1L1,GOLGB1,ARHGAP35,HIF1AN,KSR2,LIMD1,
MLEC,PDPK1,TGOLN2,TMED2,UNC119B,ZKSCAN1,ZNF740
ACOT4,AGPAT3,COPA,FBXW2,GPAM,HIPK2,HK2,
KCTD21,KIAA0100,MAPK10,SLC25A51,MLEC,PBLD,PCYOX1,
PIGS,RAB2A,SLC16A2,MIEF1,SNX19,SORT1,UNC13B

AACS,AIM1,ANKRD52,ATP2A2,BEND3,BRI3BP,CAMKK2,
CS,DDX54,DHX37,GCN1L1,HIRA,LPIN1,LRIG3,
MLEC,MLXIP,PGAM5,PKP2,POLE,POLR3B,UNC119B
BEND3,C9orf129,CDT1,CENPF,DARS2,DNAJC16,EFTUD2,
FAM120A,CLUH,LARS2,MCCC2,METTL13,MLEC,PIGO,
POLR3B,PROM2,SPTLC2,STEAP3,TARS2,TP53,TPX2
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 MLEC


There's no related Drug.
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Cross referenced IDs for MLEC
* 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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