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 EIF2S3
Basic gene info.Gene symbolEIF2S3
Gene nameeukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa
SynonymsEIF2|EIF2G|EIF2gamma|eIF-2gA
CytomapUCSC genome browser: Xp22.2-p22.1
Genomic locationchrX :24073064-24096927
Type of geneprotein-coding
RefGenesNM_001415.3,
Ensembl idENSG00000130741
DescriptioneIF-2-gamma XeIF-2gXeukaryotic translation initiation factor 2 subunit 3eukaryotic translation initiation factor 2 subunit gamma Xeukaryotic translation initiation factor 2G
Modification date20141207
dbXrefs MIM : 300161
HGNC : HGNC
HPRD : 02155
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF2S3
BioGPS: 1968
Gene Expression Atlas: ENSG00000130741
The Human Protein Atlas: ENSG00000130741
PathwayNCI Pathway Interaction Database: EIF2S3
KEGG: EIF2S3
REACTOME: EIF2S3
ConsensusPathDB
Pathway Commons: EIF2S3
MetabolismMetaCyc: EIF2S3
HUMANCyc: EIF2S3
RegulationEnsembl's Regulation: ENSG00000130741
miRBase: chrX :24,073,064-24,096,927
TargetScan: NM_001415
cisRED: ENSG00000130741
ContextiHOP: EIF2S3
cancer metabolism search in PubMed: EIF2S3
UCL Cancer Institute: EIF2S3
Assigned class in ccmGDBC

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Phenotypic Information for EIF2S3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF2S3
Familial Cancer Database: EIF2S3
* 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: EIF2S3
MedGen: EIF2S3 (Human Medical Genetics with Condition)
ClinVar: EIF2S3
PhenotypeMGI: EIF2S3 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF2S3

Mutations for EIF2S3
* 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 EIF2S3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI830759EIF2S31163X2409506424095226HNRNPA31574192178087487178087749
CB131978ZNF48020225195281915452824975EIF2S3223378X2409621424096369
BE177610SLC19A223521169434289169434644EIF2S3347525X2408620224089828
AW580222GFPT13349426955977669560231EIF2S3491623X2408055124080683
BG774247EIF2S3102142X2409588424095924H191432981120189042019057
BM969453WDR7036940853738926937389308EIF2S3405611X2409504524095251

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=24)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr23:24075780-24075780p.R98W2
chr23:24086216-24086216p.G335S2
chr23:24075797-24075797p.R103R2
chr23:24089747-24089747p.G362A2
chr23:24084129-24084129p.D263H2
chr23:24086170-24086170p.V319V2
chr23:24086182-24086182p.A323A1
chr23:24091292-24091292p.D423Y1
chr23:24082408-24082408p.I243T1
chr23:24091340-24091341p.I441fs*41

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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
# sample22232  111 31   11 9
# mutation22232  111 31   11 9
nonsynonymous SNV22221  1 1 3     1 7
synonymous SNV   11   1   1   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
chrX:24078247p.M142I1
chrX:24086218p.D423Y1
chrX:24078262p.N147N1
chrX:24089770p.R452C1
chrX:24073092p.E205K1
chrX:24080667p.K466N1
chrX:24089815p.I243T1
chrX:24073154p.D470Y1
chrX:24082408p.E253K1
chrX:24091214p.P254T1

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 EIF2S3 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 EIF2S3

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

APOO,CTPS2,EIF1AX,EIF2A,EIF2S3,KLHL15,MED14,
MRPL3,MRPL37,NPM1,OFD1,OLA1,PIGA,POLA1,
RAB9A,RSL1D1,SMS,SYAP1,TRAPPC2,TXLNG,USP9X
CCT4,CEP57,EIF2A,EIF2S3,EIF3E,EIF3L,EIF3M,
LTA4H,NAP1L1,LRRC75A-AS1,PABPC1,PCBP2,PMPCB,RPL15,
RPL22,RSL24D1,SUPT3H,TATDN1,TIMM9,TOMM20,ZNF277

APOO,CTPS2,EIF1AX,EIF2S3,FUNDC1,GEMIN8,HCCS,
HSD17B10,MCTS1,MED14,NONO,OFD1,PDHA1,JADE3,
RBBP7,RPS4X,SCML1,SMS,SYAP1,TRAPPC2,TXLNG
SMG8,CREBL2,EIF2S3,EIF3H,EIF4B,IMPDH2,KBTBD7,
LTA4H,MANBA,PAIP2B,PNLIPRP3,RPL22,RPS4X,RRAGD,
TXNDC16,WDR48,ZNF607,ZNF619,ZNF780A,ZXDA,ZXDB
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 EIF2S3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDaapproved; investigationalSirolimus


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Cross referenced IDs for EIF2S3
* 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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