Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	EIF2S2
	Gene name	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa
	Synonyms	EIF2\|EIF2B\|EIF2beta\|PPP1R67\|eIF-2-beta
	Cytomap	UCSC genome browser: 20q11.2
	Genomic location	chr20 :32676114-32700085
	Type of gene	protein-coding
	RefGenes	NM_003908.3,
	Ensembl id	ENSG00000125977
	Description	eukaryotic translation initiation factor 2 subunit 2eukaryotic translation initiation factor 2 subunit betaprotein phosphatase 1, regulatory subunit 67
	Modification date	20141207
dbXrefs	MIM : 603908
	HGNC : HGNC
	Ensembl : ENSG00000125977
	HPRD : 04882
	Vega : OTTHUMG00000032287
Protein	UniProt: P20042 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF2S2
	BioGPS: 8894
	Gene Expression Atlas: ENSG00000125977
	The Human Protein Atlas: ENSG00000125977
Pathway	NCI Pathway Interaction Database: EIF2S2
	KEGG: EIF2S2
	REACTOME: EIF2S2
	ConsensusPathDB
	Pathway Commons: EIF2S2
Metabolism	MetaCyc: EIF2S2
	HUMANCyc: EIF2S2
Regulation	Ensembl's Regulation: ENSG00000125977
	miRBase: chr20 :32,676,114-32,700,085
	TargetScan: NM_003908
	cisRED: ENSG00000125977
Context	iHOP: EIF2S2
	cancer metabolism search in PubMed: EIF2S2
	UCL Cancer Institute: EIF2S2
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF2S2 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	603908; gene.
Orphanet
Disease	KEGG Disease: EIF2S2
	MedGen: EIF2S2 (Human Medical Genetics with Condition)
	ClinVar: EIF2S2
Phenotype	MGI: EIF2S2 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	EIF2S2	chr20	32689346	32689366	EIF2S2	chr20	32695252	32695272

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF2S2 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BM837359	EIF2S2	1	250	20	32693234	32700033	TP53I11	247	689	11	44955863	44956305
BU543690	APLP2	1	694	11	129939810	129991623	EIF2S2	691	880	20	32691291	32693280

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr20:32677685-32677685	p.R285R	3
chr20:32684576-32684576	p.K190N	3
chr20:32693352-32693352	p.?	2
chr20:32677564-32677564	p.R325Q	2
chr20:32681530-32681530	p.R231C	2
chr20:32677589-32677589	p.G317C	2
chr20:32693273-32693273	p.Q32fs*39	2
chr20:32677677-32677677	p.P287P	1
chr20:32684602-32684602	p.R182*	1
chr20:32699916-32699916	p.M1L	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		2		1	1		1		1			1	1	1				4	1	6
# mutation		2		1	1		1		1			1	1	1				4	1	5
nonsynonymous SNV		2		1	1		1		1				1	1				3	1	5
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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr20:32684576	p.K190N	3
chr20:32677564	p.R325Q	2
chr20:32681530	p.L180L	1
chr20:32684501	p.I157M	1
chr20:32684509	p.M24I	1
chr20:32684518	p.M1L	1
chr20:32677582	p.Q319R	1
chr20:32677584	p.F318L	1
chr20:32684606	p.R296Q	1
chr20:32677651	p.R296G	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA27696; -.
Organism-specific databases	CTD	8894; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00877	eukaryotic translation initiation factor 2, subunit 2 beta, 38kDa	approved; investigational	Sirolimus

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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