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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: EIF4B (NCBI Gene ID:1975)


Gene Summary

check button Gene Summary
Gene InformationGene Name: EIF4B
Gene ID: 1975
Gene Symbol

EIF4B

Gene ID

1975

Gene Nameeukaryotic translation initiation factor 4B
SynonymsEIF-4B|PRO1843
Cytomap

12q13.13

Type of Geneprotein-coding
Descriptioneukaryotic translation initiation factor 4B
Modification date20200313
UniProtAcc

P23588


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0006417Regulation of translation
GO:0008135Translation factor activity, RNA binding
GO:0002181Cytoplasmic translation
GO:0006413Translational initiation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25
EIF4B(733 - 1119.25]


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Translation Studies in PubMed

check button We searched PubMed using 'EIF4B[title] AND translation [title] AND human.'
GeneTitlePMID
EIF4BeIF4B phosphorylation at Ser504 links synaptic activity with protein translation in physiology and pathology28874824


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Exon Skipping Events

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.
all structure

check button Open reading frame (ORF) analsis of exon skipping events based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF
ENST000002620565341369353413810In-frame
ENST000002620565341627653416411In-frame
ENST000002620565342156553421703In-frame
ENST000002620565343119253431406Frame-shift
ENST000002620565343302153433127Frame-shift
ENST000002620565343341353433486Frame-shift

check button Exon skipping position in the amino acid sequence.
ENSTExon skip start (DNA)Exon Skip end (DNA)Len(transcript seq)Exon skip start (mRNA)Exon Skip end (mRNA)Len(amino acid seq)Exon skip start (AA)Exon Skip end (AA)
ENST0000026205653413693534138104165687803611120159
ENST0000026205653416276534164114165859993611177222
ENST00000262056534215655342170341659941131611222268

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.
P235881772221611ChainID=PRO_0000081616;Note=Eukaryotic translation initiation factor 4B
P235881201591611ChainID=PRO_0000081616;Note=Eukaryotic translation initiation factor 4B
P235882222681611ChainID=PRO_0000081616;Note=Eukaryotic translation initiation factor 4B
P2358812015996173DomainNote=RRM;Ontology_term=ECO:0000255;evidence=ECO:0000255|PROSITE-ProRule:PRU00176
P23588177222164331Compositional biasNote=Arg-rich
P23588222268164331Compositional biasNote=Arg-rich
P23588177222169325Compositional biasNote=Asp-rich
P23588222268169325Compositional biasNote=Asp-rich
P23588177222192192Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:20068231,PMID:23186163
P23588177222207207Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244;evidence=ECO:0000244|PubMed:23186163;Dbxref=PMID:23186163
P23588177222219219Modified residueNote=Phosphoserine;Ontology_term=ECO:0000244,ECO:0000244,ECO:0000244;evidence=ECO:0000244|PubMed:18669648,ECO:0000244|PubMed:20068231,ECO:0000244|PubMed:23186163;Dbxref=PMID:18669648,PMID:20068231,PMID:23186163
P23588120159121159Alternative sequenceID=VSP_057351;Note=In isoform 2. Missing;Ontology_term=ECO:0000303;evidence=ECO:0000303|PubMed:14702039;Dbxref=PMID:14702039
P23588177222203203Natural variantID=VAR_064710;Note=Found in a renal cell carcinoma case%3B somatic mutation. P->R;Ontology_term=ECO:0000269;evidence=ECO:0000269|PubMed:21248752;Dbxref=PMID:21248752
P23588222268246246Sequence conflictNote=R->C;Ontology_term=ECO:0000305;evidence=ECO:0000305
P23588120159121125Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WI8
P23588120159130133TurnOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:2J76
P23588120159140146Beta strandOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WI8
P23588120159147154HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WI8
P23588120159155157HelixOntology_term=ECO:0000244;evidence=ECO:0000244|PDB:1WI8


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
all structure

check buttonExpression level of gene isoforms across TCGA pancancer
all structure

check buttonExpression level of gene isoforms across GTEx pantissue
all structure

check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
all structure

check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval
BRCAEIF4B-2.160327420296962.35556737304054e-22
KIRCEIF4B1.149971405104747.59366366705366e-09


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
GBMEIF4Bhsa-miR-185-5p9410.0166666666666667
UCECEIF4Bhsa-miR-185-5p94-0.3448433919022150.0464108520833579


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
all structure
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a
LUSCEIF4B210.04884643583889310.2136601702127660.1673759119496860.1003893107312220.043691412296842
SARCEIF4B210.03926246242300680.2244995811518320.1660574358974360.008094091838482720.097534989945601

check buttonTranslation factor expression regulation through copy number variation of Translation factor
all structure
Cancer typeGeneCoefficientPvalue
LIHCEIF4B0.0467863270.018955082
CHOLEIF4B0.0446990990.048740155

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with EIF4B (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)
Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure

check buttonOverlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
all structure
check button
* Edge colors based on TCGA cancer types.

check button* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
KIRCEIF4BRPS6-3.45560582778030.0001224322154943
LUADEIF4BEIF4A21.83597858364480.000162905479402723
PRADEIF4BRPS6KB11.250475019811980.000199084406212897
PRADEIF4BEIF3A1.136803283919520.000363360004697762
BRCAEIF4BEIF5-1.167043162138850.00107943958337404
COADEIF4BRPS6KB1-1.11330695676780.00144392251968384
THCAEIF4BRPS61.463461436653890.00305071956645465
CHOLEIF4BPABPC1-4.562725288153530.00390625
KIRPEIF4BEIF3G-2.41783229621290.00471024587750435
BLCAEIF4BEIF3A-4.451040583077470.00532913208007812
KICHEIF4BEIF4G1-1.466560811507430.00612920522689819
KIRPEIF4BRPS6-1.153609078341590.0111397774890065
COADEIF4BRPS61.033795895208510.011966735124588
BLCAEIF4BRPS6-1.769407775799380.012359619140625
BLCAEIF4BPABPC11.314853027927460.0180816650390625
HNSCEIF4BRPS6KB1-1.279968097050290.0301271170746986
UCECEIF4BEIF3G-3.350783346965710.03125
BLCAEIF4BEIF3G-3.077075596490910.0323410034179688
ESCAEIF4BEIF4A1-1.245380731992850.0419921875
BRCAEIF4BEIF3G1.879483850112711.9107949115022e-06
KIRPEIF4BRPS6KB1-1.464654742843482.00420618057251e-06
LIHCEIF4BPABPC1-1.720769613621882.98009622125841e-06
LIHCEIF4BEIF5-2.120604053828544.66164898670786e-08
KICHEIF4BEIF4E1.616752105626716.55651092529297e-06
BRCAEIF4BEIF3A-1.2182155731487.39403582934137e-06
KICHEIF4BEIF4A11.144855833095718.16583633422851e-06
PRADEIF4BPABPC1-2.102003183634768.55379952759014e-07


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with EIF4B
PABPC1, EIF3B, EIF4B, EIF3A, EIF3F, USP11, USP7, ALK, KBTBD7, AGO3, AGO4, Ccdc15, ELAVL1, ARRB1, ARRB2, TSG101, TERF1, TINF2, ACD, POT1, CUL3, EIF4A1, EIF4G1, RPL29, PHAX, EIF4G2, MYH9, CSTF2, NUP107, NUP153, SLC4A1AP, CCT6B, POLR1C, MAGOH, EIF4A3, SMURF1, YWHAE, CSNK2A1, PAN2, FBXO6, PARK2, Stk11, CTNNA1, CUL4B, NARS, OSBP, SAMHD1, SEC23A, XRCC5, PRMT3, SF1, XPO7, ASB2, ZBTB1, SMAD3, FBXW11, MAEL, CCT6A, CFL1, CTPS1, DDX39A, DOHH, LASP1, GSPT1, HSPB1, IMPDH2, KHSRP, SFN, YWHAQ, YWHAZ, NTRK1, gag, SRPK2, XPO1, HIST1H3E, AHSA1, CDC25B, ERCC6L, Crebbp, Smad3, Pten, Wiz, Naa10, Tmed10, Ttll12, GAN, RHOU, RC3H1, CDH1, EGFR, CYLD, TRIM25, G3BP1, YAP1, OTUD6B, GRHPR, UBE2M, EFTUD2, TNIP2, RNF31, SNAI1, RECQL4, GPC1, KCNJ2, ZFP36L2, METTL3, METTL14, KIAA1429, ALB, ANKRD53, ARPC5, BAZ2A, C14orf166, RTCB, CDON, DDX1, DDX3X, DDX3Y, DENND1C, DLEC1, DSG4, EIF3D, EIF3E, EIF3G, EIF3H, EIF3I, EIF3J, EIF3K, EIF3L, FAM98A, FEZF2, FGF11, HIST1H4A, HNRNPA1, HNRNPD, HNRNPU, HSPA1A, HSPA6, HSPA8, MRPS23, PRMT1, RBM12B, RBMX, RPL14, RPL18, RPL22, RPL23A, RPL24, RPL31, RPL9, RPS10, RPS11, RPS12, RPS13, RPS14, RPS15A, RPS16, RPS17, RPS18, RPS19, RPS20, RPS23, RPS24, RPS25, RPS26, RPS3, RPS3A, RPS4X, RPS5, RPS6, RPS7, RPS8, RPS9, RPSAP58, SRSF3, SLC45A3, SNRPD1, SNRPD3, SNRPN, SRSF9, TMEM232, TNFAIP1, TRAPPC8, USP9Y, USP9X, EIF3C, EIF3M, RC3H2, ATG16L1, GBF1, DCAF15, BICD2, PSMD14, DYRK1A, nsp8ab, SQSTM1, PLEKHA4, PINK1, LINC01554, TRIM6, DOK2, RAB5A, KIAA1211L, GATAD2A, PHACTR1, nsp1, ESR1, LAMTOR5, EIF4A2, CHMP4C, PRNP, FASN, HNRNPH1, INS, Rnf183, BRD4, CIC, Apc2, RBM39, FBP1, CSPG4, IFI16, GRB7, TXNIP, TBK1, IKBKE, PRDM13, TDRD5, PLK4, UFL1, TP53, SERBP1, FZR1, PAGE4, NUDCD2, NAA40, NIF3L1, RANBP10, NCOA5, NLRP7, AGO2, TOLLIP, SLFN11, MAGEL2,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples

check buttonCopy number variation (CNV) of EIF4B
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across EIF4B
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


check button Fusion genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
101952STADTCGA-D7-A4YTADAP1chr7994031-EIF4Bchr1253427589+
101952STADTCGA-D7-A4YT-01AADAP1chr7985398-EIF4Bchr1253427590+
101952STADTCGA-D7-A4YT-01AADAP1chr7994032-EIF4Bchr1253427590+
92821STADTCGA-D7-A4YTEIF4Bchr1253421972+ADAP1chr7975141-
25966HNSCTCGA-BA-5152EIF4Bchr1253400280+C19orf71chr193543232+
82974STADTCGA-D7-A4YT-01AEIF4Bchr1253421972+COX19chr7975141-
85888N/ABF340503EIF4Bchr1253435988+FAM53Cchr5137678717+
95270N/ABF829819EIF4Bchr1253435656+KMT2Dchr1249431501-
80172N/AAA736805EIF4Bchr1253435937+LHFPL3chr7104311984-
103326ESCATCGA-R6-A6L6EIF4Bchr1253416411+RNPC3chr1104097655+
103283UCECTCGA-EO-A3AYEIF4Bchr1253431406+RPLP0chr12120635265-
85320N/ABG213873EIF4Bchr1253408728+TNNC1chr352486122+
101952N/ABF882453FYTTD1chr3197481885+EIF4Bchr1253435318+
101952N/ABI491355MYL1chr2211171731+EIF4Bchr1253435993-
101952N/AFN093739SEMA5Achr59496148+EIF4Bchr1253435058+
101952SKCMTCGA-EE-A29D-06ATMTC3chr1288570096-EIF4Bchr1253410257+
101955N/AAW386153ZNF384chr126775904-EIF4Bchr1253433209-


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
all structure
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
TGCTEIF4B0.03068056194716560.86
LUADEIF4B0.04251355704234561

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
LUADEIF4B0.002593918376601880.086
LGGEIF4B0.02101502983097770.67
THYMEIF4B0.03835574362673721
SARCEIF4B0.04270721286442061

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source
C0041696Unipolar Depression1PSYGENET
C1269683Major Depressive Disorder1PSYGENET