Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	MLEC
	Gene name	malectin
	Synonyms	KIAA0152
	Cytomap	UCSC genome browser: 12q24.31
	Genomic location	chr12 :121124948-121139667
	Type of gene	protein-coding
	RefGenes	NM_014730.2,
	Ensembl id	ENSG00000110917
	Description	oligosaccharyltransferase complex subunit (non-catalytic)
	Modification date	20141207
dbXrefs	MIM : 613802
	HGNC : HGNC
	Ensembl : ENSG00000110917
	HPRD : 13781
	Vega : OTTHUMG00000169187
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_MLEC
	BioGPS: 9761
	Gene Expression Atlas: ENSG00000110917
	The Human Protein Atlas: ENSG00000110917
Pathway	NCI Pathway Interaction Database: MLEC
	KEGG: MLEC
	REACTOME: MLEC
	ConsensusPathDB
	Pathway Commons: MLEC
Metabolism	MetaCyc: MLEC
	HUMANCyc: MLEC
Regulation	Ensembl's Regulation: ENSG00000110917
	miRBase: chr12 :121,124,948-121,139,667
	TargetScan: NM_014730
	cisRED: ENSG00000110917
Context	iHOP: MLEC
	cancer metabolism search in PubMed: MLEC
	UCL Cancer Institute: MLEC
Assigned class in ccmGDB	C

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Phenotypic Information for MLEC(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: MLEC
	MedGen: MLEC (Human Medical Genetics with Condition)
	ClinVar: MLEC
Phenotype	MGI: MLEC (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows MLEC 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
AI632281	TERF1	1	61	8	73958605	73958665	MLEC	52	386	12	121135317	121135651
BE550278	TERF1	1	61	8	73958605	73958665	MLEC	52	385	12	121135317	121135651
AI656269	TERF1	1	61	8	73958605	73958665	MLEC	52	385	12	121135317	121135651
AI962170	TERF1	1	61	8	73958605	73958665	MLEC	52	386	12	121135317	121135651
BE501371	TERF1	1	61	8	73958605	73958665	MLEC	52	385	12	121135317	121135651
BG955818	MUC5B	11	210	11	1271330	1271533	MLEC	202	403	12	121139214	121139415
AI825089	TERF1	1	61	8	73958605	73958665	MLEC	52	290	12	121135412	121135651
AA243990	MLEC	8	158	12	121139379	121139529	MLEC	157	450	12	121139070	121139364
BF806090	MLEC	8	292	12	121125681	121125966	MAGI1	287	553	3	65720244	65720510
AA244053	MLEC	1	383	12	121138982	121139364	MLEC	382	493	12	121139418	121139529
BE930957	MOB3B	35	136	9	27393376	27393478	MLEC	129	470	12	121134483	121134823
AI651406	TXNDC9	1	351	2	99953945	99977642	MLEC	346	374	12	121137167	121137195

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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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

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr12:121132050-121132050	p.Y131C	2
chr12:121134166-121134168	p.E233delE	2
chr12:121134168-121134168	p.E233E	2
chr12:121132708-121132708	p.D166N	2
chr12:121131987-121131987	p.G110V	1
chr12:121134267-121134267	p.S266S	1
chr12:121132754-121132754	p.Q181R	1
chr12:121132937-121132937	p.M211V	1
chr12:121131998-121131998	p.P114S	1
chr12:121134306-121134306	p.F279F	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	2	1		8			1		1			6	3	1		1	1	2		3
# mutation	2	1		8			1		1			6	3	1		1	1	2		3
nonsynonymous SNV	1	1		6			1		1			5	2	1		1	1	1		2
synonymous SNV	1			2								1	1					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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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
chr12:121132708	p.D166N	2
chr12:121131964	p.G110V	1
chr12:121132899	p.E233E	1
chr12:121134306	p.S135Y	1
chr12:121131965	p.R253W	1
chr12:121132904	p.Q136K	1
chr12:121131966	p.R253P	1
chr12:121132906	p.V139L	1
chr12:121131987	p.F279F	1
chr12:121132908	p.K177T	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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