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 EIF3B

Basic gene info.	Gene symbol	EIF3B
	Gene name	eukaryotic translation initiation factor 3, subunit B
	Synonyms	EIF3-ETA\|EIF3-P110\|EIF3-P116\|EIF3S9\|PRT1
	Cytomap	UCSC genome browser: 7p22.3
	Genomic location	chr7 :2394473-2420377
	Type of gene	protein-coding
	RefGenes	NM_001037283.1, NM_003751.3,
	Ensembl id	ENSG00000106263
	Description	eIF-3-etaeIF3 p110eIF3 p116eukaryotic translation initiation factor 3 subunit 9eukaryotic translation initiation factor 3 subunit Beukaryotic translation initiation factor 3, subunit 9 (eta, 116kD)eukaryotic translation initiation factor 3, subunit
	Modification date	20141207
dbXrefs	MIM : 603917
	HGNC : HGNC
	Ensembl : ENSG00000106263
	HPRD : 06795
	Vega : OTTHUMG00000022839
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3B
	BioGPS: 8662
	Gene Expression Atlas: ENSG00000106263
	The Human Protein Atlas: ENSG00000106263
Pathway	NCI Pathway Interaction Database: EIF3B
	KEGG: EIF3B
	REACTOME: EIF3B
	ConsensusPathDB
	Pathway Commons: EIF3B
Metabolism	MetaCyc: EIF3B
	HUMANCyc: EIF3B
Regulation	Ensembl's Regulation: ENSG00000106263
	miRBase: chr7 :2,394,473-2,420,377
	TargetScan: NM_001037283
	cisRED: ENSG00000106263
Context	iHOP: EIF3B
	cancer metabolism search in PubMed: EIF3B
	UCL Cancer Institute: EIF3B
Assigned class in ccmGDB	C

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Phenotypic Information for EIF3B(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF3B
	Familial Cancer Database: EIF3B

* 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: EIF3B
	MedGen: EIF3B (Human Medical Genetics with Condition)
	ClinVar: EIF3B
Phenotype	MGI: EIF3B (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF3B

Mutations for EIF3B

* 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
pancreas	EIF3B	chr7	2417053	2417253	EIF3B	chr7	2417723	2417923

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 EIF3B 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
BI010845	EIF3B	21	152	7	2418772	2419055	POLA2	146	303	11	65047202	65047359
BF812060	EIF3B	1	289	7	2408040	2408331	FAM107B	275	448	10	14633560	14633732
AW368037	EIF3B	7	164	7	2418767	2419075	EIF3B	163	522	7	2409262	2415052
AI909918	PLEKHF1	1	52	19	30166214	30166265	EIF3B	44	187	7	2419072	2419982
BQ376118	EIF3B	1	333	7	2411532	2411865	COL6A6	323	515	3	130311389	130312095
BF813428	ERGIC1	1	87	5	172336727	172341765	EIF3B	84	139	7	2419937	2419992
AW855179	EIF3B	32	348	7	2405457	2405778	HSPG2	336	416	1	22178575	22178654
BG253176	EIF3B	23	76	7	2418349	2418402	EIF3B	64	774	7	2418354	2420380
CN267276	EIF3B	23	83	7	2402295	2402355	EIF3B	82	681	7	2402339	2409314
BF813436	EIF3B	1	253	7	2416672	2419055	EIF3B	252	303	7	2419064	2419115

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=44)	Stat. for Synonymous SNVs (# total SNVs=15)

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
chr7:2394991-2394991	p.N145N	3
chr7:2394746-2394746	p.S64P	2
chr7:2406181-2406181	p.F437L	2
chr7:2404086-2404086	p.W360L	2
chr7:2409115-2409115	p.S471Y	2
chr7:2402723-2402723	p.D277D	2
chr7:2418375-2418375	p.R736C	2
chr7:2403339-2403339	p.R315C	1
chr7:2412393-2412393	p.F591F	1
chr7:2406159-2406159	p.?	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	1	8	1		3		2			6	4	2			9	7		10
# mutation		2	1	9	1		3		2			6	4	2			10	8		13
nonsynonymous SNV		1		8	1		3					4	3	1			7	6		7
synonymous SNV		1	1	1					2			2	1	1			3	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])

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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
chr7:2402723	p.R736C,EIF3B	2
chr7:2418375	p.S471F,EIF3B	2
chr7:2409115	p.D277E,EIF3B	2
chr7:2406673	p.L359L,EIF3B	1
chr7:2416670	p.G536G,EIF3B	1
chr7:2411432	p.T644M,EIF3B	1
chr7:2414218	p.S422R,EIF3B	1
chr7:2406679	p.E545D,EIF3B	1
chr7:2412331	p.V667I,EIF3B	1
chr7:2402736	p.A424V,EIF3B	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 EIF3B 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 EIF3B

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


AIMP2,ATAD3A,C7orf26,COX19,ECE2,EIF3B,FTSJ2, GET4,INTS1,MAD1L1,MRPL12,MRPL4,MRPS24,NUDT1, POLD2,PPAN,PSMG3,RRP1,SNX8,TBRG4,WIPI2	ALKBH2,APRT,VPS51___IFT46,CCT3,CECR5,DDX54,EEF2, EIF3B,EXOSC5,MRTO4,NLE1,NOB1,PES1,PHB2, QARS,RPL19,RPL3,RPL7A,RUVBL2,SHMT2,SMARCD2

BRAT1,MALSU1,CCT6A,DAGLB,DDX56,EIF2AK1,EIF3B, FTSJ2,GARS,GET4,GGCT,HEATR2,INTS1,AP5Z1, MIOS,MRPS17,PMS2,POLD2,TBRG4,YKT6,ZMIZ2	DIS3L2,DOHH,EIF3B,EIF4G1,ELAVL1,HIRA,HNRNPA0, HNRNPM,KHSRP,LAS1L,MYBBP1A,NAT10,NOC2L,NUP188, RANGAP1,RRP12,SF3B3,SLC7A1,TBL3,TMEM201,VARS

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 EIF3B

There's no related Drug.

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Cross referenced IDs for EIF3B

* 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