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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 METTL2B

Basic gene info.	Gene symbol	METTL2B
	Gene name	methyltransferase like 2B
	Synonyms	METL\|METTL2\|METTL2A\|PSENIP1
	Cytomap	UCSC genome browser: 7q32.1
	Genomic location	chr7 :128116782-128142978
	Type of gene	protein-coding
	RefGenes	NM_018396.2,
	Ensembl id	ENSG00000165055
	Description	methyltransferase-like protein 2B
	Modification date	20141207
dbXrefs	MIM : 607846
	HGNC : HGNC
	Ensembl : ENSG00000165055
	HPRD : 09705
	Vega : OTTHUMG00000143738
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_METTL2B
	BioGPS: 55798
	Gene Expression Atlas: ENSG00000165055
	The Human Protein Atlas: ENSG00000165055
Pathway	NCI Pathway Interaction Database: METTL2B
	KEGG: METTL2B
	REACTOME: METTL2B
	ConsensusPathDB
	Pathway Commons: METTL2B
Metabolism	MetaCyc: METTL2B
	HUMANCyc: METTL2B
Regulation	Ensembl's Regulation: ENSG00000165055
	miRBase: chr7 :128,116,782-128,142,978
	TargetScan: NM_018396
	cisRED: ENSG00000165055
Context	iHOP: METTL2B
	cancer metabolism search in PubMed: METTL2B
	UCL Cancer Institute: METTL2B
Assigned class in ccmGDB	C

Top

Phenotypic Information for METTL2B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: METTL2B
	Familial Cancer Database: METTL2B

* 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
KEGG_HISTIDINE_METABOLISM KEGG_TYROSINE_METABOLISM KEGG_SELENOAMINO_ACID_METABOLISM

Others
OMIM
Orphanet
Disease	KEGG Disease: METTL2B
	MedGen: METTL2B (Human Medical Genetics with Condition)
	ClinVar: METTL2B
Phenotype	MGI: METTL2B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: METTL2B

Mutations for METTL2B

* 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

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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	METTL2B	chr7	128119073	128119093		chr7	128160801	128160821

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 METTL2B related fusion information.

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

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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)

Top

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=3

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=24)	Stat. for Synonymous SNVs (# total SNVs=13)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr7:128140982-128140982	p.Y314Y	3
chr7:128119424-128119424	p.E139K	2
chr7:128128217-128128217	p.?	2
chr7:128119514-128119514	p.E169K	2
chr7:128119380-128119380	p.C124S	2
chr7:128119262-128119262	p.H85Y	1
chr7:128138196-128138196	p.G306R	1
chr7:128141918-128141918	p.R362L	1
chr7:128120717-128120717	p.G192E	1
chr7:128119264-128119264	p.H85H	1

Top

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	1	3	2	3			1					6	2			1	9	1	1	5
# mutation	1	3	2	3			1					7	2			1	9	1	1	5
nonsynonymous SNV	1	2	1	3			1					5	1			1	8	1	1	3
synonymous SNV		1	1									2	1				1			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])

Top

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
chr7:128119262	p.H85Y	1
chr7:128141876	p.L168M	1
chr7:128119443	p.R348H	1
chr7:128133877	p.H85H	1
chr7:128119264	p.S179L	1
chr7:128141917	p.R362W	1
chr7:128119449	p.F89L	1
chr7:128133883	p.E186Q	1
chr7:128119274	p.R362L	1
chr7:128141918	p.K91K	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 METTL2B 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]

Top

Gene Expression for METTL2B

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


DLD,GCC1,KLHDC10,LMBR1,LUC7L2,LUZP6,METTL2B, NOM1,NUP205,PEX1,PUS7,RBM28,RINT1,TMEM209, TNPO3,TRRAP,UBE2H,UBE3C,WASL,ZC3HAV1L,ZNF800	AGO3,GOLGA4,IPP,KLHDC10,METTL2B,MPHOSPH9,MUT, OPA1,PBRM1,PIK3CA,PTPN4,RAPGEF2,ROCK2,RPS6KC1, RSC1A1,SAMD8,SLC25A46,TTC37,UBXN2A,USP16,YPEL2

AHCY,C12orf29,C6orf57,CAPZA2,CHCHD3,DBF4,GATC, GPN1,GTPBP10,METTL2A,METTL2B,MRPL49,ORC5,PMPCB, PMS2P1,PNO1,POT1,PUS7,RHEB,RINT1,ZNF800	C1orf174,DCAF13,DNAJA3,GNL3,INTS10,LYRM2,METTL2B, MRPL3,MRTO4,NUP35,PDCD2,POLR1C,POLR2D,PRMT3, SRPRB,TAF9,TFB2M,THUMPD3,TMEM165,UTP18,UTP6

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for METTL2B

There's no related Drug.

Top

Cross referenced IDs for METTL2B

* 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