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 FBXW4
Basic gene info.Gene symbolFBXW4
Gene nameF-box and WD repeat domain containing 4
SynonymsDAC|FBW4|FBWD4|SHFM3|SHSF3
CytomapUCSC genome browser: 10q24
Genomic locationchr10 :103370420-103454743
Type of geneprotein-coding
RefGenesNM_022039.3,
Ensembl idENSG00000107829
DescriptionF-box and WD-40 domain protein 4F-box and WD-40 domain-containing protein 4F-box/WD repeat protein 4F-box/WD repeat-containing protein 4dactylin
Modification date20141207
dbXrefs MIM : 608071
HGNC : HGNC
Ensembl : ENSG00000107829
HPRD : 06994
Vega : OTTHUMG00000018938
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FBXW4
BioGPS: 6468
Gene Expression Atlas: ENSG00000107829
The Human Protein Atlas: ENSG00000107829
PathwayNCI Pathway Interaction Database: FBXW4
KEGG: FBXW4
REACTOME: FBXW4
ConsensusPathDB
Pathway Commons: FBXW4
MetabolismMetaCyc: FBXW4
HUMANCyc: FBXW4
RegulationEnsembl's Regulation: ENSG00000107829
miRBase: chr10 :103,370,420-103,454,743
TargetScan: NM_022039
cisRED: ENSG00000107829
ContextiHOP: FBXW4
cancer metabolism search in PubMed: FBXW4
UCL Cancer Institute: FBXW4
Assigned class in ccmGDBC

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Phenotypic Information for FBXW4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FBXW4
Familial Cancer Database: FBXW4
* 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: FBXW4
MedGen: FBXW4 (Human Medical Genetics with Condition)
ClinVar: FBXW4
PhenotypeMGI: FBXW4 (International Mouse Phenotyping Consortium)
PhenomicDB: FBXW4

Mutations for FBXW4
* 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
ovaryFBXW4chr10103389288103389308BTRCchr10103285019103285039
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 FBXW4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA640671FBXW4230510103411280103411583ANKRD443054012197969512197969608
BF851864B4GALT52219204827691848277135FBXW421237310103432775103433376
BI050753FBXW4621210103387379103387585SLC16A12083191113489160113489319

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
Stat. for Synonymous SNVs
(# total SNVs=14)
Stat. for Deletions
(# total SNVs=3)
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
chr10:103433355-103433355p.F144F3
chr10:103371071-103371071p.V406I3
chr10:103371150-103371150p.S379S2
chr10:103372106-103372106p.R322H2
chr10:103371430-103371430p.Y358Y2
chr10:103432713-103432713p.G212R2
chr10:103436203-103436203p.?2
chr10:103384540-103384540p.C266C1
chr10:103371089-103371089p.L400M1
chr10:103432772-103432772p.S192N1

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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
# sample11 5  1    511  64 7
# mutation11 5  1    511  54 7
nonsynonymous SNV1  2  1    411  22 2
synonymous SNV 1 3       1    32 5
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
chr10:103433355p.F144F3
chr10:103372106p.R322H2
chr10:103371150p.S379S2
chr10:103433373p.E333K1
chr10:103371165p.S324S1
chr10:103384540p.F138F1
chr10:103436138p.G106W1
chr10:103371405p.V97V1
chr10:103384561p.P304P1
chr10:103436163p.R96L1

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 FBXW4 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 FBXW4

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

ACBD4,C14orf79,CCDC159,CCDC24,CHCHD5,CIRBP,CUEDC2,
MZT2B,FBXL15,FBXW4,FIS1,FRAT1,GAMT,MGMT,
MRPL43,MYL5,NOXA1,POLL,RAB17,TMEM219,ZNF688
BOLA1,TSR3,CHMP2A,DRG2,FBXW4,FKBP8,MRPL43,
MRPL55,PEX14,PSMD9,R3HCC1,RAB1B,NELFE,RFNG,
STUB1,TMEM187,TMEM222,USE1,WDR13,ZFAND2B,ZFPL1

C10orf95,C14orf93,C21orf2,CIRBP,CTDSP1,DNAJC4,FAM83E,
FBXW4,DICER1-AS1,FRAT1,GLTSCR2,LOC729234,LRSAM1,LZTS2,
NOXA1,POLL,PWWP2B,SLC25A28,TMEM44,TRIM8,TRAPPC12
BCAS3,CDIPT,CIZ1,CLCN7,CTDSP1,DYRK1B,FBXW4,
FOXK1,FOXO4,HDAC5,NCOR2,OTUD5,PRPF6,SNX33,
SORBS3,SUN2,TADA2B,USP19,WDTC1,ZNF213,ZNF358
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 FBXW4


There's no related Drug.
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Cross referenced IDs for FBXW4
* 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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