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 EIF2S3

Basic gene info.	Gene symbol	EIF2S3
	Gene name	eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa
	Synonyms	EIF2\|EIF2G\|EIF2gamma\|eIF-2gA
	Cytomap	UCSC genome browser: Xp22.2-p22.1
	Genomic location	chrX :24073064-24096927
	Type of gene	protein-coding
	RefGenes	NM_001415.3,
	Ensembl id	ENSG00000130741
	Description	eIF-2-gamma XeIF-2gXeukaryotic translation initiation factor 2 subunit 3eukaryotic translation initiation factor 2 subunit gamma Xeukaryotic translation initiation factor 2G
	Modification date	20141207
dbXrefs	MIM : 300161
	HGNC : HGNC
	HPRD : 02155
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF2S3
	BioGPS: 1968
	Gene Expression Atlas: ENSG00000130741
	The Human Protein Atlas: ENSG00000130741
Pathway	NCI Pathway Interaction Database: EIF2S3
	KEGG: EIF2S3
	REACTOME: EIF2S3
	ConsensusPathDB
	Pathway Commons: EIF2S3
Metabolism	MetaCyc: EIF2S3
	HUMANCyc: EIF2S3
Regulation	Ensembl's Regulation: ENSG00000130741
	miRBase: chrX :24,073,064-24,096,927
	TargetScan: NM_001415
	cisRED: ENSG00000130741
Context	iHOP: EIF2S3
	cancer metabolism search in PubMed: EIF2S3
	UCL Cancer Institute: EIF2S3
Assigned class in ccmGDB	C

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Phenotypic Information for EIF2S3(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: EIF2S3
	MedGen: EIF2S3 (Human Medical Genetics with Condition)
	ClinVar: EIF2S3
Phenotype	MGI: EIF2S3 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF2S3 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
AI830759	EIF2S3	1	163	X	24095064	24095226	HNRNPA3	157	419	2	178087487	178087749
CB131978	ZNF480	20	225	19	52819154	52824975	EIF2S3	223	378	X	24096214	24096369
BE177610	SLC19A2	2	352	1	169434289	169434644	EIF2S3	347	525	X	24086202	24089828
AW580222	GFPT1	33	494	2	69559776	69560231	EIF2S3	491	623	X	24080551	24080683
BG774247	EIF2S3	102	142	X	24095884	24095924	H19	143	298	11	2018904	2019057
BM969453	WDR70	369	408	5	37389269	37389308	EIF2S3	405	611	X	24095045	24095251

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=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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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
chr23:24075780-24075780	p.R98W	2
chr23:24086216-24086216	p.G335S	2
chr23:24075797-24075797	p.R103R	2
chr23:24089747-24089747	p.G362A	2
chr23:24084129-24084129	p.D263H	2
chr23:24086170-24086170	p.V319V	2
chr23:24086182-24086182	p.A323A	1
chr23:24091292-24091292	p.D423Y	1
chr23:24082408-24082408	p.I243T	1
chr23:24091340-24091341	p.I441fs*4	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=2

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	2	2	3	2			1	1	1		3	1				1	1		9
# mutation	2	2	2	3	2			1	1	1		3	1				1	1		9
nonsynonymous SNV	2	2	2	2	1			1		1		3						1		7
synonymous SNV				1	1				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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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
chrX:24078247	p.M142I	1
chrX:24086218	p.D423Y	1
chrX:24078262	p.N147N	1
chrX:24089770	p.R452C	1
chrX:24073092	p.E205K	1
chrX:24080667	p.K466N	1
chrX:24089815	p.I243T	1
chrX:24073154	p.D470Y	1
chrX:24082408	p.E253K	1
chrX:24091214	p.P254T	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 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

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


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

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 EIF2S3

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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 3 gamma, 52kDa	approved; investigational	Sirolimus

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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