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 EIF2S1
Basic gene info.Gene symbolEIF2S1
Gene nameeukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa
SynonymsEIF-2|EIF-2A|EIF-2alpha|EIF2|EIF2A
CytomapUCSC genome browser: 14q23.3
Genomic locationchr14 :67827033-67853233
Type of geneprotein-coding
RefGenesNM_004094.4,
Ensembl idENSG00000134001
DescriptioneIF-2-alphaeukaryotic translation initiation factor 2 subunit 1eukaryotic translation initiation factor 2 subunit alpha
Modification date20141207
dbXrefs MIM : 603907
HGNC : HGNC
Ensembl : ENSG00000134001
HPRD : 04881
Vega : OTTHUMG00000029800
ProteinUniProt: P05198
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF2S1
BioGPS: 1965
Gene Expression Atlas: ENSG00000134001
The Human Protein Atlas: ENSG00000134001
PathwayNCI Pathway Interaction Database: EIF2S1
KEGG: EIF2S1
REACTOME: EIF2S1
ConsensusPathDB
Pathway Commons: EIF2S1
MetabolismMetaCyc: EIF2S1
HUMANCyc: EIF2S1
RegulationEnsembl's Regulation: ENSG00000134001
miRBase: chr14 :67,827,033-67,853,233
TargetScan: NM_004094
cisRED: ENSG00000134001
ContextiHOP: EIF2S1
cancer metabolism search in PubMed: EIF2S1
UCL Cancer Institute: EIF2S1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF2S1 in cancer cell metabolism1. Garcia-Navas R, Munder M, Mollinedo F (2012) Depletion of L-arginine induces autophagy as a cytoprotective response to endoplasmic reticulum stress in human T lymphocytes. Autophagy 8: 1557-1576. doi: 10.4161/auto.21315. pmid: 3494587. go to article
2. Dey S, Tameire F, Koumenis C (2013) PERK-ing up autophagy during MYC-induced tumorigenesis. Autophagy 9: 612-614. doi: 10.4161/auto.23486. pmid: 3627677. go to article

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Phenotypic Information for EIF2S1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF2S1
Familial Cancer Database: EIF2S1
* 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 603907; gene.
Orphanet
DiseaseKEGG Disease: EIF2S1
MedGen: EIF2S1 (Human Medical Genetics with Condition)
ClinVar: EIF2S1
PhenotypeMGI: EIF2S1 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF2S1

Mutations for EIF2S1
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEIF2S1chr146784662867846648chr159612776996127789
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 EIF2S1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI114762EIF2S1196146782710467831509STX129073312814934328149990
CA450266EIF2S117213146785038167850577EIF2S1207302146785030667850401

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=17)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr14:67831488-67831488p.P2S2
chr14:67831527-67831527p.E15K2
chr14:67847450-67847450p.R183H2
chr14:67847476-67847476p.R192*2
chr14:67850120-67850120p.D304G1
chr14:67847477-67847477p.R192Q1
chr14:67848323-67848323p.A198A1
chr14:67831577-67831577p.G31G1
chr14:67848325-67848325p.C199F1
chr14:67831653-67831653p.R57C1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 134  3 11  11  12 1
# mutation 134  3 11  11  12 1
nonsynonymous SNV 133  1 1    1  12 1
synonymous SNV   1  2  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
chr14:67831488p.L184F1
chr14:67848323p.R192Q1
chr14:67831504p.A198A1
chr14:67848335p.Y202Y1
chr14:67831577p.M1V1
chr14:67850056p.E283K1
chr14:67831653p.M1T1
chr14:67850070p.A287A1
chr14:67831709p.M1I1
chr14:67850119p.D304H1

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 EIF2S1 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 EIF2S1

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

ATP6V1D,GSKIP,CPSF2,DLST,EIF2S1,EXOC5,FCF1,
AREL1,MED6,MTHFD1,PAPOLA,PLEK2,PPP2R5E,RDH11,
SNAPC1,SNW1,TRMT5,TTLL5,VTI1B,WDR89,ZNF410
ARL5A,ARPP19,C2orf69,CAPZA2,DPH3,EIF2S1,EIF4G2,
EXOC5,PAIP1,PCGF6,PPP6C,RAB6A,RAD23B,RNF11,
SLAIN2,SMAP1,STRAP,UBE2V2,USP14,VAMP7,VPS37A

CDKN3,CNIH1,EIF2B2,EIF2S1,ERH,G2E3,GMFB,
GNPNAT1,L2HGDH,MED6,MTHFD1,PNP,POLE2,LRR1,
PRMT5,PSMA3,PSMA6,PSMC6,TMX1,TRMT5,VRK1
ABCE1,BCCIP,BRIX1,MCMBP,TEX30,CCT2,CIRH1A,
DCUN1D5,EEF1E1,EIF2B3,EIF2S1,FASTKD2,LOC441089,LTV1,
MAGOHB,MRPS17,PNO1,PPIL1,PSMD6,SRSF3,STRAP
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 EIF2S1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL1255131; -.
Organism-specific databasesPharmGKB PA27695; -.
Organism-specific databasesCTD 1965; -.

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 1 alpha, 35kDaapproved; investigationalSirolimus


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Cross referenced IDs for EIF2S1
* 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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