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 EIF2S1

Basic gene info.	Gene symbol	EIF2S1
	Gene name	eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa
	Synonyms	EIF-2\|EIF-2A\|EIF-2alpha\|EIF2\|EIF2A
	Cytomap	UCSC genome browser: 14q23.3
	Genomic location	chr14 :67827033-67853233
	Type of gene	protein-coding
	RefGenes	NM_004094.4,
	Ensembl id	ENSG00000134001
	Description	eIF-2-alphaeukaryotic translation initiation factor 2 subunit 1eukaryotic translation initiation factor 2 subunit alpha
	Modification date	20141207
dbXrefs	MIM : 603907
	HGNC : HGNC
	Ensembl : ENSG00000134001
	HPRD : 04881
	Vega : OTTHUMG00000029800
Protein	UniProt: P05198 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF2S1
	BioGPS: 1965
	Gene Expression Atlas: ENSG00000134001
	The Human Protein Atlas: ENSG00000134001
Pathway	NCI Pathway Interaction Database: EIF2S1
	KEGG: EIF2S1
	REACTOME: EIF2S1
	ConsensusPathDB
	Pathway Commons: EIF2S1
Metabolism	MetaCyc: EIF2S1
	HUMANCyc: EIF2S1
Regulation	Ensembl's Regulation: ENSG00000134001
	miRBase: chr14 :67,827,033-67,853,233
	TargetScan: NM_004094
	cisRED: ENSG00000134001
Context	iHOP: EIF2S1
	cancer metabolism search in PubMed: EIF2S1
	UCL Cancer Institute: EIF2S1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF2S1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	603907; gene.
Orphanet
Disease	KEGG Disease: EIF2S1
	MedGen: EIF2S1 (Human Medical Genetics with Condition)
	ClinVar: EIF2S1
Phenotype	MGI: EIF2S1 (International Mouse Phenotyping Consortium)
Phenotype	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.

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

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	EIF2S1	chr14	67846628	67846648		chr15	96127769	96127789

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 EIF2S1 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
AI114762	EIF2S1	1	96	14	67827104	67831509	STX12	90	733	1	28149343	28149990
CA450266	EIF2S1	17	213	14	67850381	67850577	EIF2S1	207	302	14	67850306	67850401

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

There's no copy number variation information in COSMIC data for this gene.

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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=3

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Somatic 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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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
chr14:67847450-67847450	p.R183H	2
chr14:67847476-67847476	p.R192*	2
chr14:67831488-67831488	p.P2S	2
chr14:67831527-67831527	p.E15K	2
chr14:67848323-67848323	p.A198A	1
chr14:67831577-67831577	p.G31G	1
chr14:67848325-67848325	p.C199F	1
chr14:67831653-67831653	p.R57C	1
chr14:67848328-67848328	p.Y200F	1
chr14:67831719-67831719	p.E79Q	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		1	3	4			3		1	1			1	1			1	2		1
# mutation		1	3	4			3		1	1			1	1			1	2		1
nonsynonymous SNV		1	3	3			1		1					1			1	2		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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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
chr14:67848335	p.R75S	1
chr14:67831577	p.E79Q	1
chr14:67850056	p.L85V	1
chr14:67831653	p.Y109H	1
chr14:67850070	p.A156A	1
chr14:67831709	p.L184F	1
chr14:67850119	p.R192Q	1
chr14:67831719	p.A198A	1
chr14:67841196	p.Y202Y	1
chr14:67843159	p.M1V	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 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

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


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

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 EIF2S1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	ChEMBL	CHEMBL1255131; -.
Organism-specific databases	PharmGKB	PA27695; -.
Organism-specific databases	CTD	1965; -.

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 1 alpha, 35kDa	approved; investigational	Sirolimus

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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