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 EIF3H
Basic gene info.Gene symbolEIF3H
Gene nameeukaryotic translation initiation factor 3, subunit H
SynonymsEIF3S3|eIF3-gamma|eIF3-p40
CytomapUCSC genome browser: 8q24.11
Genomic locationchr8 :117657054-117768062
Type of geneprotein-coding
RefGenesNM_003756.2,
Ensembl idENSG00000147677
DescriptioneIF-3-gammaeIF3 p40 subuniteukaryotic translation initiation factor 3 subunit 3eukaryotic translation initiation factor 3 subunit Heukaryotic translation initiation factor 3, subunit 2 (beta, 36kD)eukaryotic translation initiation factor 3, subunit 3
Modification date20141207
dbXrefs MIM : 603912
HGNC : HGNC
Ensembl : ENSG00000147677
HPRD : 04885
ProteinUniProt: O15372
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_EIF3H
BioGPS: 8667
Gene Expression Atlas: ENSG00000147677
The Human Protein Atlas: ENSG00000147677
PathwayNCI Pathway Interaction Database: EIF3H
KEGG: EIF3H
REACTOME: EIF3H
ConsensusPathDB
Pathway Commons: EIF3H
MetabolismMetaCyc: EIF3H
HUMANCyc: EIF3H
RegulationEnsembl's Regulation: ENSG00000147677
miRBase: chr8 :117,657,054-117,768,062
TargetScan: NM_003756
cisRED: ENSG00000147677
ContextiHOP: EIF3H
cancer metabolism search in PubMed: EIF3H
UCL Cancer Institute: EIF3H
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of EIF3H in cancer cell metabolism1. Pittman AM, Naranjo S, Jalava SE, Twiss P, Ma Y, et al. (2010) Allelic variation at the 8q23.3 colorectal cancer risk locus functions as a cis-acting regulator of EIF3H. PLoS Genet 6: e1001126. doi: 10.1371/journal.pgen.1001126. pmid: 2940760. go to article
2. Lee JP, Brauweiler A, Rudolph M, Hooper JE, Drabkin HA, et al. (2010) The TRC8 ubiquitin ligase is sterol regulated and interacts with lipid and protein biosynthetic pathways. Mol Cancer Res 8: 93-106. doi: 10.1158/1541-7786.MCR-08-0491. pmid: 3086825. go to article
3. Zhang L, Smit-McBride Z, Pan X, Rheinhardt J, Hershey JW (2008) An oncogenic role for the phosphorylated h-subunit of human translation initiation factor eIF3. J Biol Chem 283: 24047-24060. doi: 10.1074/jbc.M800956200. pmid: 2527115. go to article

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Phenotypic Information for EIF3H(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: EIF3H
Familial Cancer Database: EIF3H
* 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 603912; gene.
Orphanet
DiseaseKEGG Disease: EIF3H
MedGen: EIF3H (Human Medical Genetics with Condition)
ClinVar: EIF3H
PhenotypeMGI: EIF3H (International Mouse Phenotyping Consortium)
PhenomicDB: EIF3H

Mutations for EIF3H
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
pancreasEIF3Hchr8117718770117718790EIF3Hchr8117725072117725092
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 EIF3H related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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 # sample4       2 1      
GAIN (# sample)4       2 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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=24)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr8:117738327-117738327p.E73K3
chr8:117658833-117658833p.R280C3
chr8:117658786-117658786p.P295P1
chr8:117668111-117668111p.L231I1
chr8:117671117-117671117p.R131L1
chr8:117658799-117658799p.R291L1
chr8:117738329-117738329p.V72G1
chr8:117668194-117668194p.I203T1
chr8:117671195-117671195p.R105Q1
chr8:117658800-117658800p.R291*1

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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   31 4    33   1513
# mutation   31 4    33   1513
nonsynonymous SNV   11      22   1313
synonymous SNV   2  4    11    2  
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
chr8:117658786p.P295P2
chr8:117658799p.K227K1
chr8:117671153p.L164L1
chr8:117658816p.I151M1
chr8:117671196p.L150L1
chr8:117658825p.Y140N1
chr8:117738277p.S136S1
chr8:117668111p.P310P1
chr8:117738327p.R131L1
chr8:117668121p.P308Q1

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 EIF3H 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 EIF3H

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

C8orf76,COPS5,DCAF13,EBAG9,EIF3E,EIF3H,RMDN1,
IGFBP5,MRPL13,MRPS28,NSMCE2,POLR2K,RAD21,TMEM70,
TRPS1,EMC2,TTTY2,UTP23,WDYHV1,ZFAND1,ZNF706
BTF3,C11orf1,CCT4,DPH5,EEF1A1,EIF3H,EIF3M,
RPL15,RPL22,RPL23A,RPL26,RPL30,RPL35A,RPL38,
RPL41,RPL6,RPS13,RPS15A,RPS29,RPS3A,RSL24D1

ANKRD46,AZIN1,NDUFAF6,C8orf59,COPS5,DCAF13,DPY19L4,
EBAG9,EIF3E,EIF3H,MED30,MTERF3,PABPC1,RPL30,
RPL8,RPS20,SLC25A32,TATDN1,EMC2,UTP23,ZFAND1
ATP5G2,C6orf48,CLNS1A,EEF1A1,EEF1G,EIF3D,EIF3H,
EIF3L,GNB2L1,NACA,RPL10,RPL14,RPL23A,RPL30,
RPL3,RPL38,RPL6,RPS23,RPS25,RSL1D1,TOMM20
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 EIF3H


There's no related Drug.
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Cross referenced IDs for EIF3H
* 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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