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 EEF1D

Basic gene info.	Gene symbol	EEF1D
	Gene name	eukaryotic translation elongation factor 1 delta (guanine nucleotide exchange protein)
	Synonyms	EF-1D\|EF1D\|FP1047
	Cytomap	UCSC genome browser: 8q24.3
	Genomic location	chr8 :144661866-144679845
	Type of gene	protein-coding
	RefGenes	NM_001130053.2, NM_001130055.2,NM_001130056.2,NM_001130057.2,NM_001195203.1, NM_001289950.1,NM_001960.4,NM_032378.4,NM_001130054.1,
	Ensembl id	ENSG00000104529
	Description	EF-1-deltaantigen NY-CO-4elongation factor 1-deltaguanine nucleotide exchange protein
	Modification date	20141207
dbXrefs	MIM : 130592
	HGNC : HGNC
	Ensembl : ENSG00000104529
	HPRD : 00560
	Vega : OTTHUMG00000165191
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_EEF1D
	BioGPS: 1936
	Gene Expression Atlas: ENSG00000104529
	The Human Protein Atlas: ENSG00000104529
Pathway	NCI Pathway Interaction Database: EEF1D
	KEGG: EEF1D
	REACTOME: EEF1D
	ConsensusPathDB
	Pathway Commons: EEF1D
Metabolism	MetaCyc: EEF1D
	HUMANCyc: EEF1D
Regulation	Ensembl's Regulation: ENSG00000104529
	miRBase: chr8 :144,661,866-144,679,845
	TargetScan: NM_001130053
	cisRED: ENSG00000104529
Context	iHOP: EEF1D
	cancer metabolism search in PubMed: EEF1D
	UCL Cancer Institute: EEF1D
Assigned class in ccmGDB	C

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Phenotypic Information for EEF1D(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: EEF1D
	Familial Cancer Database: EEF1D

* 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: EEF1D
	MedGen: EEF1D (Human Medical Genetics with Condition)
	ClinVar: EEF1D
Phenotype	MGI: EEF1D (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: EEF1D

Mutations for EEF1D

* 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 EEF1D 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
BF513928	EEF1D	1	155	8	144672143	144679549	EEF1D	151	519	8	144671712	144672080
BG004570	XRN2	8	163	20	21311260	21312271	EEF1D	159	283	8	144674315	144674439
BG955510	EEF1D	1	201	8	144662865	144663465	EEF1D	184	249	8	144663430	144663499
DB154094	EEF1D	1	67	8	144679517	144679583	UBE2L3	67	596	22	21947150	21976050
BQ925563	PSMB7	1	607	9	127119210	127119816	EEF1D	608	855	8	144668389	144679566
BF912863	SORT1	30	143	1	109856567	109856681	EEF1D	135	401	8	144662875	144668431
BI860302	EEF1D	1	295	8	144662237	144662830	NFKBIB	287	637	19	39398809	39399159
BG545390	B2M	2	100	15	45003715	45003812	EEF1D	95	253	8	144674959	144675116
BC034020	B2M	1	98	15	45003715	45003812	EEF1D	93	251	8	144674959	144675116
BC008012	RPL30	43	415	8	99053949	99057600	EEF1D	407	1377	8	144661898	144679574
BF513932	EEF1D	1	155	8	144672143	144679549	EEF1D	151	493	8	144671738	144672080

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=7

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=43)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=3)	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
chr8:144671244-144671244	p.R336R	7
chr8:144671685-144671685	p.D189E	6
chr8:144671277-144671277	p.A325A	2
chr8:144668984-144668984	p.I377T	2
chr8:144663466-144663466	p.S440S	2
chr8:144668985-144668985	p.I377F	2
chr8:144663282-144663282	p.R477Q	2
chr8:144663283-144663283	p.R477W	2
chr8:144668447-144668447	p.S410N	1
chr8:144671992-144671992	p.K87fs*73	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	3	3		11					2			2	1	1			2	6		7
# mutation	3	3		8					3			2	1	1			2	6		8
nonsynonymous SNV	1	1		6					2			1	1	1				4		7
synonymous SNV	2	2		2					1			1					2	2		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
chr8:144663282	p.R87Q,EEF1D	2
chr8:144663283	p.I11T,EEF1D	2
chr8:144663400	p.R87W,EEF1D	2
chr8:144668984	p.I11V,EEF1D	2
chr8:144668985	p.G72G,EEF1D	2
chr8:144671720	p.D183D,EEF1D	1
chr8:144662227	p.A51V,EEF1D	1
chr8:144668447	p.S38S,EEF1D	1
chr8:144671743	p.K164K,EEF1D	1
chr8:144662275	p.S44N,EEF1D	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 EEF1D 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 EEF1D

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


ADCK5,ANKRD19P,ARL6IP4,C19orf70,COMMD5,CYHR1,EEF1D, EXOSC4,GLI4,GSDMD,MAF1,NDUFA11,NDUFA13,NDUFB7, PUF60,PYCRL,RPL8,RPS9,SHARPIN,TIMM13,VPS28	BRMS1,C12orf10,DGCR6L,EDF1,EEF1D,EIF3G,MZT2B, FAU,MRPS26,NFKBIL1,NT5C,POLR2F,PQBP1,PRDX5, PRPF31,RFXANK,RPS15,RUVBL2,SDHAF1,STRA13,SURF2

BOP1,HGH1,COMMD5,CYC1,CYHR1,EEF1D,EIF3E, EIF3H,EXOSC4,GPAA1,HSF1,MAF1,NDUFB9,PUF60, PYCRL,RPL30,RPL8,RPS20,SHARPIN,TATDN1,TOP1MT	ARL2,C10orf35,COPRS,C20orf27,FAM229B,CAMK1,COPS7A, CUEDC2,DRAP1,EEF1D,EMD,FAM195B,IGFBP7,NDNL2, NT5C3B,PRMT2,R3HCC1,IFT22,SELM,SNRPN,UBE2D4

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 EEF1D

There's no related Drug.

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Cross referenced IDs for EEF1D

* 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