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 EIF3I

Basic gene info.	Gene symbol	EIF3I
	Gene name	eukaryotic translation initiation factor 3, subunit I
	Synonyms	EIF3S2\|PRO2242\|TRIP-1\|TRIP1\|eIF3-beta\|eIF3-p36
	Cytomap	UCSC genome browser: 1p34.1
	Genomic location	chr1 :32687970-32697205
	Type of gene	protein-coding
	RefGenes	NM_003757.2,
	Ensembl id	ENSG00000084623
	Description	TGF-beta receptor-interacting protein 1TGFbeta receptor-interacting protein 1eIF-3-betaeIF3 p36eukaryotic translation initiation factor 3 subunit 2eukaryotic translation initiation factor 3 subunit Ieukaryotic translation initiation factor 3, subuni
	Modification date	20141207
dbXrefs	MIM : 603911
	HGNC : HGNC
	Ensembl : ENSG00000084623
	HPRD : 04884
	Vega : OTTHUMG00000007364
Protein	UniProt: Q13347 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3I
	BioGPS: 8668
	Gene Expression Atlas: ENSG00000084623
	The Human Protein Atlas: ENSG00000084623
Pathway	NCI Pathway Interaction Database: EIF3I
	KEGG: EIF3I
	REACTOME: EIF3I
	ConsensusPathDB
	Pathway Commons: EIF3I
Metabolism	MetaCyc: EIF3I
	HUMANCyc: EIF3I
Regulation	Ensembl's Regulation: ENSG00000084623
	miRBase: chr1 :32,687,970-32,697,205
	TargetScan: NM_003757
	cisRED: ENSG00000084623
Context	iHOP: EIF3I
	cancer metabolism search in PubMed: EIF3I
	UCL Cancer Institute: EIF3I
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF3I in cancer cell metabolism	1. Perez RE, Navarro A, Rezaiekhaligh MH, Mabry SM, Ekekezie, II (2011) TRIP-1 regulates TGF-beta1-induced epithelial-mesenchymal transition of human lung epithelial cell line A549. Am J Physiol Lung Cell Mol Physiol 300: L799-807. doi: 10.1152/ajplung.00350.2010. go to article 2. Ahlemann M, Zeidler R, Lang S, Mack B, Munz M, et al. (2006) Carcinoma-associated eIF3i overexpression facilitates mTOR-dependent growth transformation. Mol Carcinog 45: 957-967. doi: 10.1002/mc.20269. go to article 3. Yuan Y, Zhang Y, Yao S, Shi H, Huang X, et al. (2014) The translation initiation factor eIF3i up-regulates vascular endothelial growth factor A, accelerates cell proliferation, and promotes angiogenesis in embryonic development and tumorigenesis. J Biol Chem 289: 28310-28323. doi: 10.1074/jbc.M114.571356. pmid: 4192485. go to article 4. Qi J, Dong Z, Liu J, Zhang JT (2014) EIF3i promotes colon oncogenesis by regulating COX-2 protein synthesis and beta-catenin activation. Oncogene 33: 4156-4163. doi: 10.1038/onc.2013.397. pmid: 3962800. go to article

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Phenotypic Information for EIF3I(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF3I
	Familial Cancer Database: EIF3I

* 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	603911; gene.
Orphanet
Disease	KEGG Disease: EIF3I
	MedGen: EIF3I (Human Medical Genetics with Condition)
	ClinVar: EIF3I
Phenotype	MGI: EIF3I (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF3I

Mutations for EIF3I

* 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 EIF3I 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
BG566325	EIF3I	2	631	1	32688014	32694172	ST5	627	674	11	8813443	8813490
AA032022	LRRC47	2	412	1	3697481	3697891	EIF3I	405	494	1	32697002	32697091
AI682532	EIF3I	27	137	1	32697093	32697203	HDAC1	123	216	1	32786061	32786517
AU123912	SNRPA	9	218	19	41263236	41265371	EIF3I	218	772	1	32688010	32692123
BC015407	MTMR9LP	1	925	1	32697345	32705863	EIF3I	924	1781	1	32694098	32697203

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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=32)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr1:32694343-32694343	p.T219A	4
chr1:32694386-32694386	p.N233S	3
chr1:32694367-32694367	p.R227W	2
chr1:32696779-32696779	p.E320D	2
chr1:32694334-32694334	p.D216Y	2
chr1:32691791-32691791	p.L90L	2
chr1:32692108-32692108	p.E169Q	1
chr1:32694349-32694349	p.E221*	1
chr1:32689715-32689715	p.D59D	1
chr1:32691860-32691860	p.D113D	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	3	4	1	6			2					3		1		1	2	6		3
# mutation	4	4	1	6			2					3		1		1	2	6		3
nonsynonymous SNV	4	4	1	5			2					2		1			2	5		2
synonymous SNV				1								1				1		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
chr1:32694367	p.R227W	2
chr1:32694336	p.S302G	1
chr1:32696723	p.D129N	1
chr1:32690056	p.S302S	1
chr1:32694340	p.Q132H	1
chr1:32696725	p.E320K	1
chr1:32691786	p.L157M	1
chr1:32694346	p.E322K	1
chr1:32696777	p.L5V	1
chr1:32691811	p.E169Q	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 EIF3I 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 EIF3I

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


ADPRHL2,AK2,DNAJC8,EIF3I,ERI3,HDAC1,MARCKSL1, MRPS15,MRTO4,NDUFS5,NUDC,PARK7,PEF1,PSMB2, RPL11,RPL24,RPS8,TRAPPC3,UQCRH,ZBTB8OS,ZCCHC17	C12orf10,CCT7,EIF3G,EIF3I,FAU,NHP2,NHP2L1, NME2,PHB2,RPL27A,RPL29,RPL35,RPL36,RPL7A, RPL8,RPLP1,RPS11,RPS15,RPS16,SARS,SNRPD2

AK2,ATP5G1,ATPIF1,AURKAIP1,EBNA1BP2,EIF3I,LAMTOR5, LSM10,MRPL20,MRPL37,MRPS15,MRTO4,PEF1,PSMA5, PSMB2,TRAPPC3,UQCRH,UQCRHL,UTP11L,ZBTB8OS,ZNF593	HYPK,CCT7,DCUN1D5,EBNA1BP2,EIF2S2,EIF3I,EIF4A1, EIF5AL1,MRPL3,MRPL52,NHP2,NHP2L1,NME1,NPM3, PPIL1,PRMT1,PSMB5,RAN,RANBP1,SNRPE,TMEM147

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 EIF3I

There's no related Drug.

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Cross referenced IDs for EIF3I

* 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