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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for EIF3F |
Basic gene info. | Gene symbol | EIF3F |
Gene name | eukaryotic translation initiation factor 3, subunit F | |
Synonyms | EIF3S5|eIF3-p47 | |
Cytomap | UCSC genome browser: 11p15.4 | |
Genomic location | chr11 :8008866-8017719 | |
Type of gene | protein-coding | |
RefGenes | NM_003754.2, | |
Ensembl id | ENSG00000175390 | |
Description | deubiquitinating enzyme eIF3feIF-3-epsiloneIF3-epsiloneukaryotic translation initiation factor 3 subunit Feukaryotic translation initiation factor 3, subunit 5 (epsilon, 47kD)eukaryotic translation initiation factor 3, subunit 5 epsilon, 47kDa | |
Modification date | 20141222 | |
dbXrefs | MIM : 603914 | |
HGNC : HGNC | ||
Ensembl : ENSG00000175390 | ||
HPRD : 04887 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_EIF3F | |
BioGPS: 8665 | ||
Gene Expression Atlas: ENSG00000175390 | ||
The Human Protein Atlas: ENSG00000175390 | ||
Pathway | NCI Pathway Interaction Database: EIF3F | |
KEGG: EIF3F | ||
REACTOME: EIF3F | ||
ConsensusPathDB | ||
Pathway Commons: EIF3F | ||
Metabolism | MetaCyc: EIF3F | |
HUMANCyc: EIF3F | ||
Regulation | Ensembl's Regulation: ENSG00000175390 | |
miRBase: chr11 :8,008,866-8,017,719 | ||
TargetScan: NM_003754 | ||
cisRED: ENSG00000175390 | ||
Context | iHOP: EIF3F | |
cancer metabolism search in PubMed: EIF3F | ||
UCL Cancer Institute: EIF3F | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for EIF3F(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: EIF3F |
Familial Cancer Database: EIF3F |
* This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in |
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: EIF3F |
MedGen: EIF3F (Human Medical Genetics with Condition) | |
ClinVar: EIF3F | |
Phenotype | MGI: EIF3F (International Mouse Phenotyping Consortium) |
PhenomicDB: EIF3F |
Mutations for EIF3F |
* 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 EIF3F 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 |
Other DBs for Structural Variants |
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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 | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=15) | (# total SNVs=3) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr11:8016557-8016557 | p.S258S | 2 |
chr11:8014480-8014480 | p.E188K | 1 |
chr11:8016828-8016828 | p.V304L | 1 |
chr11:8013337-8013337 | p.D125V | 1 |
chr11:8014500-8014500 | p.A194A | 1 |
chr11:8016841-8016841 | p.L308P | 1 |
chr11:8013365-8013365 | p.C134* | 1 |
chr11:8015971-8015971 | p.? | 1 |
chr11:8016859-8016859 | p.Q314R | 1 |
chr11:8013380-8013380 | p.H139H | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 | 1 | 1 |   | 5 |   |   |   |   | 1 |   |   | 3 | 1 |   |   |   | 5 | 5 | 1 | 2 |
# mutation | 1 | 1 |   | 5 |   |   |   |   | 1 |   |   | 4 | 1 |   |   |   | 5 | 5 | 1 | 2 |
nonsynonymous SNV | 1 |   |   | 3 |   |   |   |   | 1 |   |   | 2 | 1 |   |   |   | 1 | 1 | 1 | 2 |
synonymous SNV |   | 1 |   | 2 |   |   |   |   |   |   |   | 2 |   |   |   |   | 4 | 4 |   |   |
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 |
chr11:8016539 | p.H139H | 1 |
chr11:8013337 | p.D321H | 1 |
chr11:8016556 | p.V163V | 1 |
chr11:8013380 | p.E324E | 1 |
chr11:8016557 | p.T175P | 1 |
chr11:8013684 | p.D333N | 1 |
chr11:8016560 | p.T175M | 1 |
chr11:8014441 | p.E188K | 1 |
chr11:8016841 | p.R192R | 1 |
chr11:8014442 | p.A194A | 1 |
Other DBs for Point Mutations |
Copy Number for EIF3F 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 EIF3F |
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. |
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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 |
EIF3F,GLTSCR2,GNB2L1,RPL10,RPL10A,RPL11,RPL13A, RPL27A,RPL31,RPL34,RPL36,RPL37A,RPLP0,RPLP2, RPS13,RPS14,RPS23,RPS27A,RPS8,RPS9,RPSAP58 | EIF3F,EIF3I,EIF3K,MRPL11,MRPL9,MRPS21,PFDN5, PHB2,RPL10,RPL11,RPL24,RPL27,RPL27A,RPL29, RPL38,RPLP1,RPS11,RPS16,RPS25,SNRPD2,UBA52 |
EEF1G,EIF3F,EIF3M,GNB2L1,PGAP2,RPL13,RPL14, RPL18,RPL28,RPL29,RPL32,RPL38,RPLP2,RPS11, RPS13,RPS15,RPS25,RPS2,RPS3,RPS9,TAF10 | ALKBH7,VPS51___IFT46,NOA1,DALRD3,DNAJC4,EEF1G,EIF3D, EIF3F,GLTSCR2,GNB2L1,MACROD1,PEX10,QARS,RPL13, RPL28,RPS15,RPS2,SLC25A6,TRAPPC6A,TSEN34,ZNF524 |
Co-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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for EIF3F |
There's no related Drug. |
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Cross referenced IDs for EIF3F |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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