Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 EIF3K
Basic gene info.Gene symbolEIF3K
Gene nameeukaryotic translation initiation factor 3, subunit K
SynonymsEIF3-p28|EIF3S12|HSPC029|M9|MSTP001|PLAC-24|PLAC24|PRO1474|PTD001
CytomapUCSC genome browser: 19q13.2
Genomic locationchr19 :39109721-39127595
Type of geneprotein-coding
RefGenesNM_001300992.1,
NM_013234.3,
Ensembl idENSG00000178982
DescriptioneIF-3 p28eukaryotic translation initiation factor 3 subunit Keukaryotic translation initiation factor 3, subunit 12muscle specificmuscle-specific gene M9 protein
Modification date20141207
dbXrefs MIM : 609596
HGNC : HGNC
Ensembl : ENSG00000178982
HPRD : 11740
Vega : OTTHUMG00000180865
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3K
BioGPS: 27335
Gene Expression Atlas: ENSG00000178982
The Human Protein Atlas: ENSG00000178982
PathwayNCI Pathway Interaction Database: EIF3K
KEGG: EIF3K
REACTOME: EIF3K
ConsensusPathDB
Pathway Commons: EIF3K
MetabolismMetaCyc: EIF3K
HUMANCyc: EIF3K
RegulationEnsembl's Regulation: ENSG00000178982
miRBase: chr19 :39,109,721-39,127,595
TargetScan: NM_001300992
cisRED: ENSG00000178982
ContextiHOP: EIF3K
cancer metabolism search in PubMed: EIF3K
UCL Cancer Institute: EIF3K
Assigned class in ccmGDBC

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Phenotypic Information for EIF3K(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3K
Familial Cancer Database: EIF3K
* 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: EIF3K
MedGen: EIF3K (Human Medical Genetics with Condition)
ClinVar: EIF3K
PhenotypeMGI: EIF3K (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3K

Mutations for EIF3K
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows EIF3K related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW084209EIF3K5124193912570439127593PGK1117492X7737281077378728
BE909212SLC45A11164183979488399611EIF3K164576193910984639116742
AW498858EIF3K1110193911479939116738STMN3111162206227115862271209

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 # sample          1      
GAIN (# sample)          1      
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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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=14)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=0)
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
chr19:39114742-39114742p.Q62*2
chr19:39116687-39116687p.R100Q2
chr19:39111066-39111074p.L51_L53delLKL1
chr19:39116732-39116732p.Q115R1
chr19:39116734-39116734p.A116S1
chr19:39114749-39114749p.T64M1
chr19:39123104-39123104p.G130A1
chr19:39114750-39114750p.T64T1
chr19:39123118-39123118p.E135Q1
chr19:39114783-39114783p.T75T1

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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 1         131   2 3
# mutation 1         131   2 3
nonsynonymous SNV 1         121   1 2
synonymous SNV            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
chr19:39116687p.R100Q2
chr19:39116703p.A116S1
chr19:39116732p.G130A1
chr19:39116734p.E160G1
chr19:39123104p.I187I1
chr19:39123298p.I18V1
chr19:39125694p.E24Q1
chr19:39109960p.T75T1
chr19:39110987p.L105L1
chr19:39114783p.Q115R1

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 EIF3K 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 EIF3K

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

BPY2,C19orf33,C22orf31,COX6B1,EIF3K,FAM98C,FBL,
LIN37,MRPS12,NDUFB11,POLR2I,PPP1R14A,PSMD8,RBM42,
RPS16,SARS2,SDHAF1,TIMM50,UXT,WDR13,YIF1B
ATP5L,COPS6,COX4I1,COX6B1,EIF3F,EIF3K,FAM162A,
GRHPR,HAX1,MRPL11,MRPL20,MRPL40,MRPL43,MRPS18A,
NDUFS5,POLR2I,PSMB7,TOMM22,TOMM7,TRAPPC2L,TXN2

COX4I1,COX6B1,EIF3K,GEMIN7,ISOC2,MRPS12,NDUFA13,
NDUFB7,NDUFS7,PSMD8,RPL13A,RPL18,RPL28,RPS11,
RPS16,RPS9,SDHAF1,SNRPD2,TIMM50,TMEM147,UQCRFS1
ATP5O,C19orf70,COX4I1,CYC1,DIABLO,EIF3K,MRPL11,
MRPL15,MRPL27,NDUFA11,NDUFAB1,NDUFB4,NDUFB7,NDUFB9,
NDUFS3,PHB2,NELFE,TXN2,UQCR10,UQCRH,ZNHIT1
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 EIF3K


There's no related Drug.
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Cross referenced IDs for EIF3K
* 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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