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 EIF2B4
Basic gene info.Gene symbolEIF2B4
Gene nameeukaryotic translation initiation factor 2B, subunit 4 delta, 67kDa
SynonymsEIF-2B|EIF2B|EIF2Bdelta
CytomapUCSC genome browser: 2p23.3
Genomic locationchr2 :27587218-27592919
Type of geneprotein-coding
RefGenesNM_001034116.1,
NM_015636.3,NM_172195.3,
Ensembl idENSG00000115211
DescriptioneIF-2B GDP-GTP exchange factor subunit deltaeukaryotic translation initiation factor 2B subunit 4 deltatranslation initiation factor eIF-2B subunit deltatranslation initiation factor eIF-2b delta subunit
Modification date20141219
dbXrefs MIM : 606687
HGNC : HGNC
Ensembl : ENSG00000115211
HPRD : 09459
Vega : OTTHUMG00000151927
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF2B4
BioGPS: 8890
Gene Expression Atlas: ENSG00000115211
The Human Protein Atlas: ENSG00000115211
PathwayNCI Pathway Interaction Database: EIF2B4
KEGG: EIF2B4
REACTOME: EIF2B4
ConsensusPathDB
Pathway Commons: EIF2B4
MetabolismMetaCyc: EIF2B4
HUMANCyc: EIF2B4
RegulationEnsembl's Regulation: ENSG00000115211
miRBase: chr2 :27,587,218-27,592,919
TargetScan: NM_001034116
cisRED: ENSG00000115211
ContextiHOP: EIF2B4
cancer metabolism search in PubMed: EIF2B4
UCL Cancer Institute: EIF2B4
Assigned class in ccmGDBC

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Phenotypic Information for EIF2B4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF2B4
Familial Cancer Database: EIF2B4
* 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: EIF2B4
MedGen: EIF2B4 (Human Medical Genetics with Condition)
ClinVar: EIF2B4
PhenotypeMGI: EIF2B4 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF2B4

Mutations for EIF2B4
* 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 EIF2B4 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
There's no copy number variation information in COSMIC data for this gene.

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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=26)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr2:27591006-27591006p.S197R2
chr2:27591877-27591877p.S139fs*32
chr2:27587334-27587334p.T502M1
chr2:27591956-27591956p.R112Q1
chr2:27587741-27587741p.H406Y1
chr2:27587343-27587343p.L499P1
chr2:27591960-27591960p.E111K1
chr2:27587757-27587757p.K400K1
chr2:27591261-27591261p.N190D1
chr2:27587370-27587370p.D490A1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 114    1  3 3  15 6
# mutation 114    1  3 3  16 6
nonsynonymous SNV  12    1  3 3  15 4
synonymous SNV 1 2             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
chr2:27587326p.L519R,EIF2B41
chr2:27590037p.N210D,EIF2B41
chr2:27591981p.D510A,EIF2B41
chr2:27587343p.S159L,EIF2B41
chr2:27590347p.N498N,EIF2B41
chr2:27591996p.P158P,EIF2B41
chr2:27587370p.A492A,EIF2B41
chr2:27590383p.T157P,EIF2B41
chr2:27592363p.L477V,EIF2B41
chr2:27587405p.R132Q,EIF2B41

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 EIF2B4 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 EIF2B4

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

AUP1,AURKAIP1,C19orf24,ATRAID,PTRHD1,COMMD1,EDF1,
EIF2B4,ENDOG,GADD45GIP1,ILKAP,MRPL53,NUDC,OST4,
PREB,SNX17,SURF2,THAP3,TRAPPC12,WBP1,ZNF513
DDRGK1,DGCR6L,DRG2,EDF1,EIF2B4,FKBP2,NFKBIL1,
NT5C,NUDC,OTUD5,PIH1D1,PMVK,POLR2F,R3HCC1,
NELFE,RFXANK,SUGP1,STRA13,SURF2,TCF25,UBXN1

ATIC,AUP1,BCS1L,CAPN10,CCT7,CIAO1,CPSF3,
DDX1,EIF2B4,ERCC3,ING5,NOL10,POLG2,PREB,
PTDSS2,SMYD5,SSB,STK25,SUPT7L,TMEM150A,WDR75
ARIH2,ARL2BP,ARMC1,C11orf73,FAM216A,CDPF1,MSANTD3,
CBY1,CDKL3,DFFA,DNAJC24,EIF2B4,FAM104B,FAM92A1,
FBXO9,ITGB1BP1,SPIN2B,TPD52L2,TTC8,UBE2Q2,ZNF415
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 EIF2B4


There's no related Drug.
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Cross referenced IDs for EIF2B4
* 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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