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 FBXO4
Basic gene info.Gene symbolFBXO4
Gene nameF-box protein 4
SynonymsFBX4
CytomapUCSC genome browser: 5p12
Genomic locationchr5 :41925355-41941672
Type of geneprotein-coding
RefGenesNM_001297437.1,
NM_012176.2,NM_033484.2,
Ensembl idENSG00000151876
DescriptionF-box only protein 4F-box protein Fbx4
Modification date20141207
dbXrefs MIM : 609090
HGNC : HGNC
Ensembl : ENSG00000151876
HPRD : 09949
Vega : OTTHUMG00000094799
ProteinUniProt: Q9UKT5
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FBXO4
BioGPS: 26272
Gene Expression Atlas: ENSG00000151876
The Human Protein Atlas: ENSG00000151876
PathwayNCI Pathway Interaction Database: FBXO4
KEGG: FBXO4
REACTOME: FBXO4
ConsensusPathDB
Pathway Commons: FBXO4
MetabolismMetaCyc: FBXO4
HUMANCyc: FBXO4
RegulationEnsembl's Regulation: ENSG00000151876
miRBase: chr5 :41,925,355-41,941,672
TargetScan: NM_001297437
cisRED: ENSG00000151876
ContextiHOP: FBXO4
cancer metabolism search in PubMed: FBXO4
UCL Cancer Institute: FBXO4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for FBXO4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FBXO4
Familial Cancer Database: FBXO4
* 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 609090; gene.
Orphanet
DiseaseKEGG Disease: FBXO4
MedGen: FBXO4 (Human Medical Genetics with Condition)
ClinVar: FBXO4
PhenotypeMGI: FBXO4 (International Mouse Phenotyping Consortium)
PhenomicDB: FBXO4

Mutations for FBXO4
* 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 FBXO4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF331537NUP2101311531339281913392920FBXO410731754192616041926370
BE073326NUP210611431339281113392920FBXO410631654192616041926370
BE073423NUP210311031339281313392920FBXO410231254192616041926370

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=34)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr5:41941351-41941351p.L378I2
chr5:41929935-41929935p.E188K2
chr5:41929976-41929976p.E201D1
chr5:41941379-41941379p.R387K1
chr5:41927273-41927273p.K116K1
chr5:41934278-41934278p.N256H1
chr5:41929858-41929858p.G162E1
chr5:41939669-41939669p.F342S1
chr5:41929978-41929978p.E202V1
chr5:41941382-41941382p.*388L1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample3  7  3 3  64  114 5
# mutation3  7  3 3  94  115 5
nonsynonymous SNV3  6  1 1  74  114 4
synonymous SNV   1  2 2  2     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
chr5:41929884p.L171L,FBXO42
chr5:41934414p.I128V,FBXO41
chr5:41927307p.F231F,FBXO41
chr5:41929974p.T132A,FBXO41
chr5:41939605p.I235M,FBXO41
chr5:41927319p.A135V,FBXO41
chr5:41929975p.R241I,FBXO41
chr5:41925578p.M140L,FBXO41
chr5:41939628p.R261L,FBXO41
chr5:41927329p.A141T,FBXO41

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 FBXO4 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 FBXO4

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

LINC00467,NADK2,CCNH,CDKN2AIPNL,CMBL,COG2,COPZ1,
CYB5D2,DYNC2LI1,FBXO4,GIN1,KLHDC9,LRTOMT,MED7,
RBKS,SCCPDH,SPEF2,TMEM116,TMEM9B,XPA,ZCWPW2
C18orf32,C6orf62,CCBL2,DYNC2LI1,FBXO4,IFT52,KRCC1,
NUP54,PDCD10,PSMG2,RAB28,RFWD2,SFT2D1,SNRPB2,
TAF9,TCEA1,TMEM50B,TRIP4,UNC50,VPS26A,ZFAND1

ACN9,C5orf28,C6orf57,COMMD3,DERA,FAM96A,FBXO4,
FUNDC2,GBAS,PAIP1,PRDX4,RAD1,SLC25A5,SUB1,
TMEM218,TTC33,UXT,VPS29,WDR70,YEATS4,ZNF622
KANSL2,COA1,COPS3,ENOPH1,ENY2,ERH,FBXO4,
HAUS1,HSCB,MRPS14,NAA20,NUP54,OSTC,POLE3,
PRDX3,PRDX4,RPS7,SIVA1,SNRPD2,TOMM6,TRIAP1
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 FBXO4


There's no related Drug.
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Cross referenced IDs for FBXO4
* 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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