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 EIF3J
Basic gene info.Gene symbolEIF3J
Gene nameeukaryotic translation initiation factor 3, subunit J
SynonymsEIF3S1|eIF3-alpha|eIF3-p35
CytomapUCSC genome browser: 15q21.1
Genomic locationchr15 :44829265-44855001
Type of geneprotein-coding
RefGenesNM_001284335.1,
NM_001284336.1,NM_003758.3,
Ensembl idENSG00000104131
Descriptioneukaryotic translation initiation factor 3 subunit Jeukaryotic translation initiation factor 3, subunit 1 (alpha, 35kD)
Modification date20141207
dbXrefs MIM : 603910
HGNC : HGNC
Ensembl : ENSG00000104131
HPRD : 04883
Vega : OTTHUMG00000131158
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3J
BioGPS: 8669
Gene Expression Atlas: ENSG00000104131
The Human Protein Atlas: ENSG00000104131
PathwayNCI Pathway Interaction Database: EIF3J
KEGG: EIF3J
REACTOME: EIF3J
ConsensusPathDB
Pathway Commons: EIF3J
MetabolismMetaCyc: EIF3J
HUMANCyc: EIF3J
RegulationEnsembl's Regulation: ENSG00000104131
miRBase: chr15 :44,829,265-44,855,001
TargetScan: NM_001284335
cisRED: ENSG00000104131
ContextiHOP: EIF3J
cancer metabolism search in PubMed: EIF3J
UCL Cancer Institute: EIF3J
Assigned class in ccmGDBC

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Phenotypic Information for EIF3J(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3J
Familial Cancer Database: EIF3J
* 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: EIF3J
MedGen: EIF3J (Human Medical Genetics with Condition)
ClinVar: EIF3J
PhenotypeMGI: EIF3J (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3J

Mutations for EIF3J
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
ovaryEIF3Jchr154483660344836623chr154501571445015734
pancreasEIF3Jchr154484960144849621chr154501061145010631
prostateEIF3Jchr154483432544836325RAB5Cchr174030117040303170
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 EIF3J related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ938173EIF3J173321154484307344843721EIF3J320468154484307344843721

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=12)
Stat. for Insertions
(# total SNVs=2)

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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
chr15:44843099-44843099p.E61fs*56
chr15:44849797-44849797p.L174V3
chr15:44829394-44829395p.A8_G9insAAA2
chr15:44829395-44829397p.A8delA2
chr15:44843655-44843655p.I77fs*12
chr15:44829437-44829437p.?1
chr15:44846861-44846861p.T135T1
chr15:44853322-44853322p.V251A1
chr15:44843088-44843088p.D54D1
chr15:44849713-44849713p.D146Y1

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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
# sample2  31   1       1  5
# mutation2  41   1       1  5
nonsynonymous SNV2  31           1  4
synonymous SNV   1    1          1
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
chr15:44849735p.L125L,EIF3J1
chr15:44849770p.C139Y,EIF3J1
chr15:44849797p.L147V,EIF3J1
chr15:44849840p.I150N,EIF3J1
chr15:44852461p.L157F,EIF3J1
chr15:44829435p.G180G,EIF3J1
chr15:44852471p.D15H,EIF3J1
chr15:44843088p.D54D,EIF3J1
chr15:44852491p.A63T,EIF3J1
chr15:44843113p.K70Q,EIF3J1

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 EIF3J 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 EIF3J

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

ABCE1,AQR,DPH6,BUB1B,KNSTRN,RHOV___CHP1,COPS2,
CTDSPL2,EIF3J,ELL3,FBXO22,LOC729082,LOC729176,NIPA2,
BLOC1S6,SPATA5L1,TMOD3,TUBGCP4,UBE3A,USP8,ZNF770
FAM210A,FAM220A,CCDC43,COPS3,COPS4,E2F6,EIF3J,
FXN,GRSF1,HCCS,HINT3,MMADHC,NAA50,NDUFA5,
NDUFAF4,NT5C3A,PRKRA,PSMC6,RAB10,UBE2G1,VTA1

ANP32A,DPH6,BLM,KNSTRN,VWA9,CEBPZ,COPS2,
DUT,EIF3J,FBXO22,HAUS2,MRPL30,NIPA2,NOP58,
PDCD7,RPL4,RSL24D1,SNRPA1,SPATA5L1,WDR43,ZC3H15
ABCE1,BCCIP,BRIX1,CCT2,CCT6A,CIRH1A,DDX21,
EIF2S1,EIF3J,FASTKD2,GTPBP4,HDAC2,LTV1,NIFK,
MRPL19,NAA15,NOL10,NOP58,SEH1L,SRFBP1,WDR77
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 EIF3J


There's no related Drug.
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Cross referenced IDs for EIF3J
* 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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