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 symbolEIF3D
Gene nameeukaryotic translation initiation factor 3, subunit D
SynonymsEIF3S7|eIF3-p66|eIF3-zeta
CytomapUCSC genome browser: 22q13.1
Genomic locationchr22 :36906896-36925277
Type of geneprotein-coding
RefGenesNM_003753.3,
Ensembl idENSG00000100353
DescriptioneIF3 p66eukaryotic translation initiation factor 3 subunit Deukaryotic translation initiation factor 3, subunit 7 zeta, 66/67kDatranslation initiation factor eIF3 p66 subunit
Modification date20141207
dbXrefs MIM : 603915
HGNC : HGNC
Ensembl : ENSG00000100353
HPRD : 04888
Vega : OTTHUMG00000150599
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3D
BioGPS: 8664
Gene Expression Atlas: ENSG00000100353
The Human Protein Atlas: ENSG00000100353
PathwayNCI Pathway Interaction Database: EIF3D
KEGG: EIF3D
REACTOME: EIF3D
ConsensusPathDB
Pathway Commons: EIF3D
MetabolismMetaCyc: EIF3D
HUMANCyc: EIF3D
RegulationEnsembl's Regulation: ENSG00000100353
miRBase: chr22 :36,906,896-36,925,277
TargetScan: NM_003753
cisRED: ENSG00000100353
ContextiHOP: EIF3D
cancer metabolism search in PubMed: EIF3D
UCL Cancer Institute: EIF3D
Assigned class in ccmGDBC

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Phenotypic Information for EIF3D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: EIF3D
MedGen: EIF3D (Human Medical Genetics with Condition)
ClinVar: EIF3D
PhenotypeMGI: EIF3D (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF3D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE122841S100A282911153533821153536246EIF3D289453223690861536912655
BE260321EIF3D1337223692068136925170UCP2333633117368942673693808
BM974825EIF3D19122223690690436907007TNRC18116642753475255348795
AA463841EIF3D1211223690699336907705EIF3D207300223690771736907809
CD688331EIF3D32261223690774836908650EIF3D254558223691994236922081
BM910722PEG1018479429883794298920EIF3D81470223692064336925196
AI028447EIF3D7259223690690236907656EIF3D256369223691252536912638
BF768948EIF3D2312223691489136916733PSMD1330340411252820252921
BE122809EIF3D4163223690861536912655S100A21614441153533821153536246
BG991794EIF3D14363223691994236922128FAM111A357457115891938158919481

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1                
GAIN (# sample)                 
LOSS (# sample)1                
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr22:36921753-36921753p.A43T9
chr22:36916708-36916708p.R165C2
chr22:36919318-36919318p.R135*2
chr22:36907704-36907704p.C493C2
chr22:36920021-36920021p.L105F2
chr22:36912745-36912745p.?2
chr22:36907710-36907710p.L491L1
chr22:36920659-36920659p.R97Q1
chr22:36912753-36912753p.R359C1
chr22:36922148-36922148p.P7P1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample 217  1    31   4215
# mutation 217  1    31   4215
nonsynonymous SNV 115  1    3    3214
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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr22:36907704p.C493C2
chr22:36907688p.R97Q1
chr22:36915565p.L491L1
chr22:36922128p.D52N1
chr22:36915583p.V457M1
chr22:36907710p.P22L1
chr22:36916626p.N428D1
chr22:36907814p.V21I1
chr22:36916654p.S401S1
chr22:36908574p.A20V1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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



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