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 FBXW7
Basic gene info.Gene symbolFBXW7
Gene nameF-box and WD repeat domain containing 7, E3 ubiquitin protein ligase
SynonymsAGO|CDC4|FBW6|FBW7|FBX30|FBXO30|FBXW6|SEL-10|SEL10|hAgo|hCdc4
CytomapUCSC genome browser: 4q31.3
Genomic locationchr4 :153332311-153456393
Type of geneprotein-coding
RefGenesNM_001013415.1,
NM_001257069.1,NM_018315.4,NM_033632.3,
Ensembl idENSG00000109670
DescriptionF-box and WD-40 domain protein 7 (archipelago homolog, Drosophila)F-box protein FBW7F-box protein FBX30F-box protein SEL-10F-box/WD repeat-containing protein 7archipelagohomolog of C elegans sel-10
Modification date20141222
dbXrefs MIM : 606278
HGNC : HGNC
Ensembl : ENSG00000109670
HPRD : 05888
Vega : OTTHUMG00000185246
ProteinUniProt: Q969H0
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FBXW7
BioGPS: 55294
Gene Expression Atlas: ENSG00000109670
The Human Protein Atlas: ENSG00000109670
PathwayNCI Pathway Interaction Database: FBXW7
KEGG: FBXW7
REACTOME: FBXW7
ConsensusPathDB
Pathway Commons: FBXW7
MetabolismMetaCyc: FBXW7
HUMANCyc: FBXW7
RegulationEnsembl's Regulation: ENSG00000109670
miRBase: chr4 :153,332,311-153,456,393
TargetScan: NM_001013415
cisRED: ENSG00000109670
ContextiHOP: FBXW7
cancer metabolism search in PubMed: FBXW7
UCL Cancer Institute: FBXW7
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of FBXW7 in cancer cell metabolism1. Okazaki H, Matsunaga N, Fujioka T, Okazaki F, Akagawa Y, et al. (2014) Circadian regulation of mTOR by the ubiquitin pathway in renal cell carcinoma. Cancer Res 74: 543-551. doi: 10.1158/0008-5472.CAN-12-3241. go to article
2. Xu Y, Swartz KL, Siu KT, Bhattacharyya M, Minella AC (2014) Fbw7-dependent cyclin E regulation ensures terminal maturation of bone marrow erythroid cells by restraining oxidative metabolism. Oncogene 33: 3161-3171. doi: 10.1038/onc.2013.289. pmid: 3939062. go to article
3. Li S, Oh YT, Yue P, Khuri FR, Sun SY (2015) Inhibition of mTOR complex 2 induces GSK3/FBXW7-dependent degradation of sterol regulatory element-binding protein 1 (SREBP1) and suppresses lipogenesis in cancer cells. Oncogene. doi: 10.1038/onc.2015.123. go to article

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Phenotypic Information for FBXW7(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FBXW7
Familial Cancer Database: FBXW7
* 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 BLCA 6, COAD 7, CRC 8, LUSC 9, UCEC 10, STAD 11,

Therapeutic Vulnerabilities in Cancer12

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,
6 http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12965.html,
7 http://www.nature.com/nature/journal/v487/n7407/full/nature11252.html,
8 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
9 http://www.nature.com/nature/journal/v489/n7417/full/nature11404.html,
10 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
11 http://www.nature.com/nature/journal/v513/n7517/full/nature13480.html,
12Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM 606278; gene.
Orphanet
DiseaseKEGG Disease: FBXW7
MedGen: FBXW7 (Human Medical Genetics with Condition)
ClinVar: FBXW7
PhenotypeMGI: FBXW7 (International Mouse Phenotyping Consortium)
PhenomicDB: FBXW7

Mutations for FBXW7
* 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
breastFBXW7chr4153417751153417751chr4153462101153462101
ovaryFBXW7chr4153390842153390862chr19523678523698
ovaryFBXW7chr4153390842153390862chr19523680523700
ovaryFBXW7chr4153440103153440123FBXW7chr4153375517153375537
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 FBXW7 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DQ177302RUNX11275213621976736220044FBXW72592794153332704153332724
AI133397FBXW786074153250162153250761KLF12599820137468344574683666
BF089643FBXW7222064153244074153244258PRR4197406121099847610999779

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   2  
GAIN (# sample)              1  
LOSS (# sample)          1   1  
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=218

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=722)
Stat. for Synonymous SNVs
(# total SNVs=60)
Stat. for Deletions
(# total SNVs=17)
Stat. for Insertions
(# total SNVs=16)

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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
chr4:153249385-153249385p.R465C94
chr4:153249384-153249384p.R465H81
chr4:153247289-153247289p.R505S80
chr4:153247366-153247366p.R479L53
chr4:153247288-153247288p.R505L27
chr4:153244092-153244092p.R689W18
chr4:153245446-153245446p.S582L17
chr4:153251907-153251907p.R367*15
chr4:153258983-153258983p.R278*13
chr4:153244185-153244185p.R658*10

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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=21

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample7511301 13131 91061 919136
# mutation651971 11131 9861 1012124
nonsynonymous SNV651691 10121 6551 911123
synonymous SNV   30  1 1  331  11 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
chr4:153249385p.R347C,FBXW722
chr4:153247289p.R387G,FBXW720
chr4:153249384p.R347H,FBXW718
chr4:153247366p.R361P,FBXW78
chr4:153244092p.R571W,FBXW76
chr4:153249457p.R323W,FBXW75
chr4:153247244p.R13R,FBXW74
chr4:153249383p.E575E,FBXW74
chr4:153332917p.D402Y,FBXW74
chr4:153247288p.R387H,FBXW74

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 FBXW7 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 FBXW7

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

C10orf90,CARD6,CYYR1,DDX26B,FBXW7,FTMT,GPM6B,
HPS5,KIAA0922,KIT,OTUD4,PLCG2,PLRG1,RAPGEF2,
RGS2,S100B,SFRP1,SOX10,TANK,TIGD2,TRIM2
C15orf41,CLPX,CPEB3,CUL5,AMER1,FBXW7,GFM2,
MED14,NAA25,OTUD4,PARG,RBL1,RFESD,RFX7,
SACS,SOS2,THAP9,TLK2,UBE3A,ZBTB43,ZNF41

BTAF1,CCDC39,FBXW7,FLJ40330,GVINP1,ITK,JAK3,
KCNA3,KIAA0125,NKTR,NLRC3,P2RY8,PARP15,PPP1R16B,
PVRIG,SLFN14,TMEM156,TTN,WSB1,ZAP70,ZNF831
ANKLE2,CDV3,E2F3,FBXW7,FCRL5,EHMT1-IT1,FOXO1,
GAPVD1,GLCCI1,LRIG2,MAPK1IP1L,MON2,NCRNA00120,NUP153,
PLAC4,PSME4,PTPN1,RALGAPA1,RCOR1,SETX,SMEK1
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 FBXW7
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA28054; -.
Organism-specific databasesCTD 55294; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877F-box and WD repeat domain containing 7, E3 ubiquitin protein ligaseapproved; investigationalSirolimus


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Cross referenced IDs for FBXW7
* 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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