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 EIF4H
Basic gene info.Gene symbolEIF4H
Gene nameeukaryotic translation initiation factor 4H
SynonymsWBSCR1|WSCR1|eIF-4H
CytomapUCSC genome browser: 7q11.23
Genomic locationchr7 :73588705-73611429
Type of geneprotein-coding
RefGenesNM_022170.1,
NM_031992.1,
Ensembl idENSG00000263344
DescriptionWilliams-Beuren syndrome chromosome region 1
Modification date20141207
dbXrefs MIM : 603431
HGNC : HGNC
Ensembl : ENSG00000106682
HPRD : 11940
Vega : OTTHUMG00000023025
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF4H
BioGPS: 7458
Gene Expression Atlas: ENSG00000263344
The Human Protein Atlas: ENSG00000263344
PathwayNCI Pathway Interaction Database: EIF4H
KEGG: EIF4H
REACTOME: EIF4H
ConsensusPathDB
Pathway Commons: EIF4H
MetabolismMetaCyc: EIF4H
HUMANCyc: EIF4H
RegulationEnsembl's Regulation: ENSG00000263344
miRBase: chr7 :73,588,705-73,611,429
TargetScan: NM_022170
cisRED: ENSG00000263344
ContextiHOP: EIF4H
cancer metabolism search in PubMed: EIF4H
UCL Cancer Institute: EIF4H
Assigned class in ccmGDBC

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Phenotypic Information for EIF4H(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF4H
Familial Cancer Database: EIF4H
* 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: EIF4H
MedGen: EIF4H (Human Medical Genetics with Condition)
ClinVar: EIF4H
PhenotypeMGI: EIF4H (International Mouse Phenotyping Consortium)
PhenomicDB: EIF4H

Mutations for EIF4H
* 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
* 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryEIF4Hchr77358900673589026EIF4Hchr77358907073589090
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 EIF4H related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM479877EIF4H110777360985473609960H2AFY1008795134681668134724788
BU540394EIF4H238977361061873611005PKP338460511404687404908
CN419986RSL1D11595161193166011933835EIF4H58876577360636673606543

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
There's no copy number variation information in COSMIC data for this gene.

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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=5)
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
chr7:73609537-73609537p.R216*2
chr7:73604022-73604022p.F89F2
chr7:73609165-73609165p.P188P2
chr7:73609176-73609176p.G192E1
chr7:73588773-73588773p.?1
chr7:73604186-73604186p.A116E1
chr7:73609501-73609501p.E204Q1
chr7:73601967-73601967p.G29V1
chr7:73604591-73604591p.R142*1
chr7:73602045-73602045p.Q55R1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 42 1 11 1   12513
# mutation 1 42 1 11 1   12513
nonsynonymous SNV   22   11 1    23 2
synonymous SNV 1 2  1        1 211
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
chr7:73604022p.F89F,EIF4H3
chr7:73609165p.P168P,EIF4H2
chr7:73604598p.T38A,EIF4H1
chr7:73601967p.Q224Q,EIF4H1
chr7:73604629p.Q55R,EIF4H1
chr7:73601993p.T78A,EIF4H1
chr7:73609098p.V87L,EIF4H1
chr7:73602045p.S94F,EIF4H1
chr7:73609149p.A98P,EIF4H1
chr7:73602113p.Y101Y,EIF4H1

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 EIF4H 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 EIF4H

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

BAZ1B,BCL7B,CHN1,CLDN4,CRCP,EIF4H,GTF2I,
KRT82,LIMK1,MDH2,POM121,POM121C,POR,PSMC2,
RFC2,SBDSP1,SLC25A13,TBL2,WBSCR16,WBSCR22,YWHAG
AAMP,AATF,ARFGAP2,ARL6IP4,HYPK,OGFOD3,C6orf47,
EIF4H,HARS,HIRIP3,HNRNPUL2,IK,NT5C,NUDC,
PDAP1,PPM1G,SART1,SF3B2,TAF15,TSR2,UBXN1

ARPC1A,BAZ1B,BCL7B,COPS6,EIF4H,GNB2,GTF2I,
LMTK2,MDH2,PAXIP1,PDAP1,POM121,POM121C,SLC25A13,
TAF6,TNPO3,TRRAP,TYW1,YWHAG,ZKSCAN5,ZSCAN25
BRE,C10orf76,COL4A3BP,DDX6,DYNLL2,DYRK1A,EIF4H,
HNRNPUL2,JAK1,KIAA1279,KIF1B,LARGE,MAPK1,PAFAH1B1,
PARN,PPP2R3A,RAB3GAP1,RAD23B,RYBP,SUN2,TOX4
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 EIF4H


There's no related Drug.
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Cross referenced IDs for EIF4H
* 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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