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 METTL2B
Basic gene info.Gene symbolMETTL2B
Gene namemethyltransferase like 2B
SynonymsMETL|METTL2|METTL2A|PSENIP1
CytomapUCSC genome browser: 7q32.1
Genomic locationchr7 :128116782-128142978
Type of geneprotein-coding
RefGenesNM_018396.2,
Ensembl idENSG00000165055
Descriptionmethyltransferase-like protein 2B
Modification date20141207
dbXrefs MIM : 607846
HGNC : HGNC
Ensembl : ENSG00000165055
HPRD : 09705
Vega : OTTHUMG00000143738
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_METTL2B
BioGPS: 55798
Gene Expression Atlas: ENSG00000165055
The Human Protein Atlas: ENSG00000165055
PathwayNCI Pathway Interaction Database: METTL2B
KEGG: METTL2B
REACTOME: METTL2B
ConsensusPathDB
Pathway Commons: METTL2B
MetabolismMetaCyc: METTL2B
HUMANCyc: METTL2B
RegulationEnsembl's Regulation: ENSG00000165055
miRBase: chr7 :128,116,782-128,142,978
TargetScan: NM_018396
cisRED: ENSG00000165055
ContextiHOP: METTL2B
cancer metabolism search in PubMed: METTL2B
UCL Cancer Institute: METTL2B
Assigned class in ccmGDBC

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Phenotypic Information for METTL2B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_HISTIDINE_METABOLISM
KEGG_TYROSINE_METABOLISM
KEGG_SELENOAMINO_ACID_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: METTL2B
MedGen: METTL2B (Human Medical Genetics with Condition)
ClinVar: METTL2B
PhenotypeMGI: METTL2B (International Mouse Phenotyping Consortium)
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.

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
ovaryMETTL2Bchr7128119073128119093chr7128160801128160821
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 METTL2B 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 # sample 2               
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=3

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check002.gifSomatic 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.

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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
chr7:128140982-128140982p.Y314Y3
chr7:128119514-128119514p.E169K2
chr7:128119380-128119380p.C124S2
chr7:128119424-128119424p.E139K2
chr7:128128217-128128217p.?2
chr7:128119502-128119502p.I165F1
chr7:128133877-128133877p.P230R1
chr7:128119315-128119315p.E102E1
chr7:128141829-128141829p.T332T1
chr7:128119505-128119505p.S166G1

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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
# sample1323  1    62  19115
# mutation1323  1    72  19115
nonsynonymous SNV1213  1    51  18113
synonymous SNV 11        21   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])

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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
chr7:128119511p.N79T1
chr7:128138178p.S166G1
chr7:128119311p.G338E1
chr7:128119545p.H85Y1
chr7:128138196p.L168M1
chr7:128119315p.R348H1
chr7:128119565p.H85H1
chr7:128141820p.S179L1
chr7:128119379p.R362W1
chr7:128120717p.F89L1

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 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]

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Gene Expression for METTL2B

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

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
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 METTL2B


There's no related Drug.
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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



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