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 EIF3B
Basic gene info.Gene symbolEIF3B
Gene nameeukaryotic translation initiation factor 3, subunit B
SynonymsEIF3-ETA|EIF3-P110|EIF3-P116|EIF3S9|PRT1
CytomapUCSC genome browser: 7p22.3
Genomic locationchr7 :2394473-2420377
Type of geneprotein-coding
RefGenesNM_001037283.1,
NM_003751.3,
Ensembl idENSG00000106263
DescriptioneIF-3-etaeIF3 p110eIF3 p116eukaryotic translation initiation factor 3 subunit 9eukaryotic translation initiation factor 3 subunit Beukaryotic translation initiation factor 3, subunit 9 (eta, 116kD)eukaryotic translation initiation factor 3, subunit
Modification date20141207
dbXrefs MIM : 603917
HGNC : HGNC
Ensembl : ENSG00000106263
HPRD : 06795
Vega : OTTHUMG00000022839
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3B
BioGPS: 8662
Gene Expression Atlas: ENSG00000106263
The Human Protein Atlas: ENSG00000106263
PathwayNCI Pathway Interaction Database: EIF3B
KEGG: EIF3B
REACTOME: EIF3B
ConsensusPathDB
Pathway Commons: EIF3B
MetabolismMetaCyc: EIF3B
HUMANCyc: EIF3B
RegulationEnsembl's Regulation: ENSG00000106263
miRBase: chr7 :2,394,473-2,420,377
TargetScan: NM_001037283
cisRED: ENSG00000106263
ContextiHOP: EIF3B
cancer metabolism search in PubMed: EIF3B
UCL Cancer Institute: EIF3B
Assigned class in ccmGDBC

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Phenotypic Information for EIF3B(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3B
Familial Cancer Database: EIF3B
* 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: EIF3B
MedGen: EIF3B (Human Medical Genetics with Condition)
ClinVar: EIF3B
PhenotypeMGI: EIF3B (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3B

Mutations for EIF3B
* 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
pancreasEIF3Bchr724170532417253EIF3Bchr724177232417923
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 EIF3B related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI010845EIF3B21152724187722419055POLA2146303116504720265047359
BF812060EIF3B1289724080402408331FAM107B275448101463356014633732
AW368037EIF3B7164724187672419075EIF3B163522724092622415052
AI909918PLEKHF1152193016621430166265EIF3B44187724190722419982
BQ376118EIF3B1333724115322411865COL6A63235153130311389130312095
BF813428ERGIC11875172336727172341765EIF3B84139724199372419992
AW855179EIF3B32348724054572405778HSPG233641612217857522178654
BG253176EIF3B2376724183492418402EIF3B64774724183542420380
CN267276EIF3B2383724022952402355EIF3B82681724023392409314
BF813436EIF3B1253724166722419055EIF3B252303724190642419115

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   1         1   
GAIN (# sample)   1         1   
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=44)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr7:2394991-2394991p.N145N3
chr7:2404086-2404086p.W360L2
chr7:2409115-2409115p.S471Y2
chr7:2402723-2402723p.D277D2
chr7:2418375-2418375p.R736C2
chr7:2394746-2394746p.S64P2
chr7:2406181-2406181p.F437L2
chr7:2414218-2414218p.F622F1
chr7:2404084-2404084p.L359L1
chr7:2416670-2416670p.R705L1

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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
# sample 2181 3 2  642  97 10
# mutation 2191 3 2  642  108 13
nonsynonymous SNV 1 81 3    431  76 7
synonymous SNV 111    2  211  32 6
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
chr7:2402723p.R736C,EIF3B2
chr7:2418375p.S471F,EIF3B2
chr7:2409115p.D277E,EIF3B2
chr7:2415052p.R705L,EIF3B1
chr7:2404028p.A238A,EIF3B1
chr7:2418800p.G466W,EIF3B1
chr7:2409146p.F591F,EIF3B1
chr7:2402289p.A243D,EIF3B1
chr7:2412389p.K468Q,EIF3B1
chr7:2415065p.N597N,EIF3B1

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 EIF3B 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 EIF3B

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

AIMP2,ATAD3A,C7orf26,COX19,ECE2,EIF3B,FTSJ2,
GET4,INTS1,MAD1L1,MRPL12,MRPL4,MRPS24,NUDT1,
POLD2,PPAN,PSMG3,RRP1,SNX8,TBRG4,WIPI2
ALKBH2,APRT,VPS51___IFT46,CCT3,CECR5,DDX54,EEF2,
EIF3B,EXOSC5,MRTO4,NLE1,NOB1,PES1,PHB2,
QARS,RPL19,RPL3,RPL7A,RUVBL2,SHMT2,SMARCD2

BRAT1,MALSU1,CCT6A,DAGLB,DDX56,EIF2AK1,EIF3B,
FTSJ2,GARS,GET4,GGCT,HEATR2,INTS1,AP5Z1,
MIOS,MRPS17,PMS2,POLD2,TBRG4,YKT6,ZMIZ2
DIS3L2,DOHH,EIF3B,EIF4G1,ELAVL1,HIRA,HNRNPA0,
HNRNPM,KHSRP,LAS1L,MYBBP1A,NAT10,NOC2L,NUP188,
RANGAP1,RRP12,SF3B3,SLC7A1,TBL3,TMEM201,VARS
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 EIF3B


There's no related Drug.
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Cross referenced IDs for EIF3B
* 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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