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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 EIF3A

Basic gene info.	Gene symbol	EIF3A
	Gene name	eukaryotic translation initiation factor 3, subunit A
	Synonyms	EIF3\|EIF3S10\|P167\|TIF32\|eIF3-p170\|eIF3-theta\|p180\|p185
	Cytomap	UCSC genome browser: 10q26
	Genomic location	chr10 :120794540-120840334
	Type of gene	protein-coding
	RefGenes	NM_003750.2,
	Ensembl id	ENSG00000107581
	Description	EIF3, p180 subunitcentrosomin homologcytoplasmic protein p167eIF-3-thetaeIF3 p167eIF3 p180eIF3 p185eukaryotic translation initiation factor 3 subunit 10eukaryotic translation initiation factor 3 subunit Aeukaryotic translation initiation factor 3
	Modification date	20141207
dbXrefs	MIM : 602039
	HGNC : HGNC
	Ensembl : ENSG00000107581
	HPRD : 03618
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3A
	BioGPS: 8661
	Gene Expression Atlas: ENSG00000107581
	The Human Protein Atlas: ENSG00000107581
Pathway	NCI Pathway Interaction Database: EIF3A
	KEGG: EIF3A
	REACTOME: EIF3A
	ConsensusPathDB
	Pathway Commons: EIF3A
Metabolism	MetaCyc: EIF3A
	HUMANCyc: EIF3A
Regulation	Ensembl's Regulation: ENSG00000107581
	miRBase: chr10 :120,794,540-120,840,334
	TargetScan: NM_003750
	cisRED: ENSG00000107581
Context	iHOP: EIF3A
	cancer metabolism search in PubMed: EIF3A
	UCL Cancer Institute: EIF3A
Assigned class in ccmGDB	C

Top

Phenotypic Information for EIF3A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF3A
	Familial Cancer Database: EIF3A

* 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: EIF3A
	MedGen: EIF3A (Human Medical Genetics with Condition)
	ClinVar: EIF3A
Phenotype	MGI: EIF3A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF3A

Mutations for EIF3A

* 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

Top

- 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	EIF3A	chr10	120806586	120806606	NANOS1	chr10	120791396	120791416
ovary	EIF3A	chr10	120806586	120806606	NANOS1	chr10	120791397	120791417

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 EIF3A 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
BC014625	EIF3A	9	1071	10	120801629	120810165	CSF1R	1067	1289	5	149474470	149474693
BE797876	EIF3A	17	108	10	120801969	120802060	SMARCC1	104	888	3	47632267	47680270
DA942713	PSMD6	1	281	3	64008050	64009080	EIF3A	273	582	10	120802239	120809487
AW501580	STAG2	8	135	X	123202478	123205097	EIF3A	131	502	10	120820815	120829131
BF752470	EIF3A	1	464	10	120809314	120816354	LRRFIP1	455	587	2	238671873	238672005
BM771430	EIF3A	5	192	10	120840140	120840327	SFXN4	192	615	10	120900729	120914690
AI207430	EIF3A	1	372	10	120801566	120801937	SLCO1B1	362	658	12	21294366	21294662
BE841770	ATP2C2	18	217	16	84432115	84438833	EIF3A	215	556	10	120817711	120819163
BE706163	OOEP	26	203	6	74082859	74083034	EIF3A	201	389	10	120810761	120816367

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

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

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

Top

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

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=114)	Stat. for Synonymous SNVs (# total SNVs=28)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr10:120796639-120796639	p.R1304H	4
chr10:120801850-120801850	p.R1061H	3
chr10:120795555-120795555	p.R1382H	2
chr10:120796780-120796780	p.S1257L	2
chr10:120802195-120802195	p.R946T	2
chr10:120810775-120810775	p.R752Q	2
chr10:120825026-120825026	p.T336M	2
chr10:120801712-120801712	p.R1107Q	2
chr10:120810137-120810137	p.R790Q	2
chr10:120825029-120825029	p.R335H	2

Top

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	5	2		20	1		4		4			9	9				5	12	1	16
# mutation	5	2		25	1		5		5			13	10				10	13	1	26
nonsynonymous SNV	5	2		21			5		4			11	5				8	11	1	20
synonymous SNV				4	1				1			2	5				2	2		6

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])

Top

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
chr10:120795555	p.R172H	2
chr10:120832428	p.R1107Q	2
chr10:120802173	p.R1382H	2
chr10:120802195	p.R1000Q	2
chr10:120795718	p.R1061H	2
chr10:120801850	p.R1328S	2
chr10:120802033	p.D953D	2
chr10:120801712	p.R946T	2
chr10:120810117	p.H1011R	1
chr10:120830448	p.P913Q	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 EIF3A 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]

Top

Gene Expression for EIF3A

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


CCDC186,MCMBP,C10orf12,GPATCH11,DDX21,DHX9,EIF3A, FAM45B,GTF2A1,IDE,LMTK2,NHLRC2,PDZD8,REST, RIF1,SEC23IP,SLK,SMC3,SPEN,TGFBRAP1,YLPM1	BAZ1B,CAMSAP1,DDX42,EIF3A,ST13P4,FAM168B,GART, GATC,HDLBP,CLUH,KPNB1,LARP1,MFSD9,NUDT16, PTPRF,RNASEH1,STAT5B,THRAP3,TNPO3,TXLNG,ZBED3

ABLIM1,ANKRD17,BMS1,EIF3A,GBF1,GOLGA4,INO80, LARP1,MKI67,NSD1,PDCD11,POLR3A,PPRC1,SEC23IP, SLK,SLTM,SMC3,THRAP3,YLPM1,ZNF37A,ZNF770	ALMS1,BMS1,BPTF,CDK12,EIF3A,EP400,GCN1L1, HECTD1,HUWE1,LARP1,LRBA,MDN1,MED1,NUP214, PRKDC,RANBP2,RIF1,RRP1B,TRRAP,VPRBP,YLPM1

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for EIF3A

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 3, subunit A	approved; investigational	Sirolimus

Top

Cross referenced IDs for EIF3A

* 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