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 EIF3D

Basic gene info.	Gene symbol	EIF3D
	Gene name	eukaryotic translation initiation factor 3, subunit D
	Synonyms	EIF3S7\|eIF3-p66\|eIF3-zeta
	Cytomap	UCSC genome browser: 22q13.1
	Genomic location	chr22 :36906896-36925277
	Type of gene	protein-coding
	RefGenes	NM_003753.3,
	Ensembl id	ENSG00000100353
	Description	eIF3 p66eukaryotic translation initiation factor 3 subunit Deukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDatranslation initiation factor eIF3 p66 subunit
	Modification date	20141207
dbXrefs	MIM : 603915
	HGNC : HGNC
	Ensembl : ENSG00000100353
	HPRD : 04888
	Vega : OTTHUMG00000150599
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EIF3D
	BioGPS: 8664
	Gene Expression Atlas: ENSG00000100353
	The Human Protein Atlas: ENSG00000100353
Pathway	NCI Pathway Interaction Database: EIF3D
	KEGG: EIF3D
	REACTOME: EIF3D
	ConsensusPathDB
	Pathway Commons: EIF3D
Metabolism	MetaCyc: EIF3D
	HUMANCyc: EIF3D
Regulation	Ensembl's Regulation: ENSG00000100353
	miRBase: chr22 :36,906,896-36,925,277
	TargetScan: NM_003753
	cisRED: ENSG00000100353
Context	iHOP: EIF3D
	cancer metabolism search in PubMed: EIF3D
	UCL Cancer Institute: EIF3D
Assigned class in ccmGDB	C

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Phenotypic Information for EIF3D(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EIF3D
	Familial Cancer Database: EIF3D

* 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: EIF3D
	MedGen: EIF3D (Human Medical Genetics with Condition)
	ClinVar: EIF3D
Phenotype	MGI: EIF3D (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EIF3D

Mutations for EIF3D

* 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 EIF3D 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
BE122841	S100A2	8	291	1	153533821	153536246	EIF3D	289	453	22	36908615	36912655
BE260321	EIF3D	1	337	22	36920681	36925170	UCP2	333	633	11	73689426	73693808
BM974825	EIF3D	19	122	22	36906904	36907007	TNRC18	116	642	7	5347525	5348795
AA463841	EIF3D	1	211	22	36906993	36907705	EIF3D	207	300	22	36907717	36907809
CD688331	EIF3D	32	261	22	36907748	36908650	EIF3D	254	558	22	36919942	36922081
BM910722	PEG10	1	84	7	94298837	94298920	EIF3D	81	470	22	36920643	36925196
AI028447	EIF3D	7	259	22	36906902	36907656	EIF3D	256	369	22	36912525	36912638
BF768948	EIF3D	2	312	22	36914891	36916733	PSMD13	303	404	11	252820	252921
BE122809	EIF3D	4	163	22	36908615	36912655	S100A2	161	444	1	153533821	153536246
BG991794	EIF3D	14	363	22	36919942	36922128	FAM111A	357	457	11	58919381	58919481

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=9

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=36)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr22:36921753-36921753	p.A43T	9
chr22:36916708-36916708	p.R165C	2
chr22:36919318-36919318	p.R135*	2
chr22:36920021-36920021	p.L105F	2
chr22:36907704-36907704	p.C493C	2
chr22:36912745-36912745	p.?	2
chr22:36912804-36912804	p.P342S	1
chr22:36915530-36915530	p.T211T	1
chr22:36920665-36920665	p.R95Q	1
chr22:36907793-36907793	p.V464I	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	7			1					3	1				4	2	1	5
# mutation		2	1	7			1					3	1				4	2	1	5
nonsynonymous SNV		1	1	5			1					3					3	2	1	4
synonymous SNV		1		2									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
chr22:36907704	p.C493C	2
chr22:36915583	p.A20V	1
chr22:36907710	p.S401S	1
chr22:36916626	p.S14L	1
chr22:36907814	p.R359C	1
chr22:36916654	p.R310C	1
chr22:36908574	p.I251I	1
chr22:36916708	p.R218W	1
chr22:36912528	p.T211T	1
chr22:36920017	p.E200K	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 EIF3D 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 EIF3D

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


ADSL,ATF4,RTCB,CBY1,CSNK1E,DRG1,EIF3D, EIF3L,MCAT,NHP2L1,PES1,PHF5A,POLR2F,RPL10A, RPL3,RPL5,RPL6,RPS18,TOMM22,TXN2,XRCC6	ALKBH2,EEF1G,EIF3D,FBL,GNB2L1,IMPDH2,NOB1, RPL10,RPL10A,RPL12,RPL14,RPL3,RPL5,RPL7A, RPLP0,RPS18,RPS3,RPS4X,RPS6,RPS8,RPSAP58

ADSL,NOA1,CECR5,DRG1,EIF3D,EIF3L,HSCB, NHP2L1,NPM1,PES1,POLR2F,RPL23A,RPL34,RPL3, RPL4,RPL5,RPL6,RPS8,SMARCB1,SNRPD3,TXN2	NOA1,C6orf48,EEF1G,EIF3D,EIF3F,EIF3H,EIF3L, GLTSCR2,GNB2L1,NLE1,NOB1,QARS,RPL13,RPL18, RPL3,RPS15,RPS2,SLC25A6,THG1L,TMEM101,TSEN34

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 EIF3D

There's no related Drug.

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Cross referenced IDs for EIF3D

* 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