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 EIF2S2
Basic gene info.Gene symbolEIF2S2
Gene nameeukaryotic translation initiation factor 2, subunit 2 beta, 38kDa
SynonymsEIF2|EIF2B|EIF2beta|PPP1R67|eIF-2-beta
CytomapUCSC genome browser: 20q11.2
Genomic locationchr20 :32676114-32700085
Type of geneprotein-coding
RefGenesNM_003908.3,
Ensembl idENSG00000125977
Descriptioneukaryotic translation initiation factor 2 subunit 2eukaryotic translation initiation factor 2 subunit betaprotein phosphatase 1, regulatory subunit 67
Modification date20141207
dbXrefs MIM : 603908
HGNC : HGNC
Ensembl : ENSG00000125977
HPRD : 04882
Vega : OTTHUMG00000032287
ProteinUniProt: P20042
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF2S2
BioGPS: 8894
Gene Expression Atlas: ENSG00000125977
The Human Protein Atlas: ENSG00000125977
PathwayNCI Pathway Interaction Database: EIF2S2
KEGG: EIF2S2
REACTOME: EIF2S2
ConsensusPathDB
Pathway Commons: EIF2S2
MetabolismMetaCyc: EIF2S2
HUMANCyc: EIF2S2
RegulationEnsembl's Regulation: ENSG00000125977
miRBase: chr20 :32,676,114-32,700,085
TargetScan: NM_003908
cisRED: ENSG00000125977
ContextiHOP: EIF2S2
cancer metabolism search in PubMed: EIF2S2
UCL Cancer Institute: EIF2S2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF2S2 in cancer cell metabolism1. Heaney JD, Michelson MV, Youngren KK, Lam MY, Nadeau JH (2009) Deletion of eIF2beta suppresses testicular cancer incidence and causes recessive lethality in agouti-yellow mice. Hum Mol Genet 18: 1395-1404. doi: 10.1093/hmg/ddp045. pmid: 2664146. go to article

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Phenotypic Information for EIF2S2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF2S2
Familial Cancer Database: EIF2S2
* 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 UCEC 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 603908; gene.
Orphanet
DiseaseKEGG Disease: EIF2S2
MedGen: EIF2S2 (Human Medical Genetics with Condition)
ClinVar: EIF2S2
PhenotypeMGI: EIF2S2 (International Mouse Phenotyping Consortium)
PhenomicDB: EIF2S2

Mutations for EIF2S2
* 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
ovaryEIF2S2chr203268934632689366EIF2S2chr203269525232695272
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 EIF2S2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM837359EIF2S21250203269323432700033TP53I11247689114495586344956305
BU543690APLP2169411129939810129991623EIF2S2691880203269129132693280

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      2 1 1     1
GAIN (# sample)      2 1 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=4

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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=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr20:32684576-32684576p.K190N3
chr20:32677685-32677685p.R285R3
chr20:32681530-32681530p.R231C2
chr20:32677589-32677589p.G317C2
chr20:32693273-32693273p.Q32fs*392
chr20:32693352-32693352p.?2
chr20:32677564-32677564p.R325Q2
chr20:32678367-32678367p.R261K1
chr20:32686406-32686406p.T111P1
chr20:32677582-32677582p.Q319R1

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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 2 11 1 1  111   416
# mutation 2 11 1 1  111   415
nonsynonymous SNV 2 11 1 1   11   315
synonymous SNV           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
chr20:32684576p.K190N3
chr20:32677564p.R325Q2
chr20:32677584p.Q319R1
chr20:32684606p.F318L1
chr20:32677651p.R296Q1
chr20:32685285p.R296G1
chr20:32677652p.P287P1
chr20:32693295p.R285L1
chr20:32677677p.R261K1
chr20:32699916p.R231C1

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 EIF2S2 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 EIF2S2

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

AHCY,C20orf24,CCT4,CDK5RAP1,DSN1,E2F1,EIF2S2,
MAPRE1,MARS,PIGU,PSMA7,PSMD7,PTTG1,RALY,
RAN,RANBP1,SHMT2,TOMM22,TPX2,TUBA1C,UBE2C
ATP5E,SLIRP,CMC2,C20orf24,EIF2S2,ENY2,GTF3C6,
LSM1,LSM3,MRPL47,PSMA1,PSMA2,PSMA3,PSMA4,
PSMA6,PSMD6,TCEB1,THOC7,TTC1,UBE2F,ZBTB8OS

C20orf24,AAR2,CDK5RAP1,CSE1L,CTNNBL1,DPM1,DSN1,
EIF2S2,EIF6,TTI1,MAPRE1,MOCS3,PDRG1,PIGU,
PSMA7,RAE1,RALY,NELFCD,TP53RK,UBE2V1,UQCC1
DCUN1D5,EEF1E1,EIF2S2,EIF3I,EIF4A1,EIF5AL1,H2AFZ,
HAT1,MAGOHB,MORF4L2,PFDN2,PSMB5,PSMC2,PSMD14,
PSMD7,RAN,SNRPB2,SNRPD1,SNRPE,SSBP1,TIMM17A
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 EIF2S2
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA27696; -.
Organism-specific databasesCTD 8894; -.

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 2 beta, 38kDaapproved; investigationalSirolimus


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Cross referenced IDs for EIF2S2
* 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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