Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	FBXO4
	Gene name	F-box protein 4
	Synonyms	FBX4
	Cytomap	UCSC genome browser: 5p12
	Genomic location	chr5 :41925355-41941672
	Type of gene	protein-coding
	RefGenes	NM_001297437.1, NM_012176.2,NM_033484.2,
	Ensembl id	ENSG00000151876
	Description	F-box only protein 4F-box protein Fbx4
	Modification date	20141207
dbXrefs	MIM : 609090
	HGNC : HGNC
	Ensembl : ENSG00000151876
	HPRD : 09949
	Vega : OTTHUMG00000094799
Protein	UniProt: Q9UKT5 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_FBXO4
	BioGPS: 26272
	Gene Expression Atlas: ENSG00000151876
	The Human Protein Atlas: ENSG00000151876
Pathway	NCI Pathway Interaction Database: FBXO4
	KEGG: FBXO4
	REACTOME: FBXO4
	ConsensusPathDB
	Pathway Commons: FBXO4
Metabolism	MetaCyc: FBXO4
	HUMANCyc: FBXO4
Regulation	Ensembl's Regulation: ENSG00000151876
	miRBase: chr5 :41,925,355-41,941,672
	TargetScan: NM_001297437
	cisRED: ENSG00000151876
Context	iHOP: FBXO4
	cancer metabolism search in PubMed: FBXO4
	UCL Cancer Institute: FBXO4
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for FBXO4(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM	609090; gene.
Orphanet
Disease	KEGG Disease: FBXO4
	MedGen: FBXO4 (Human Medical Genetics with Condition)
	ClinVar: FBXO4
Phenotype	MGI: FBXO4 (International Mouse Phenotyping Consortium)
Phenotype	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.

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 FBXO4 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
BF331537	NUP210	13	115	3	13392819	13392920	FBXO4	107	317	5	41926160	41926370
BE073326	NUP210	6	114	3	13392811	13392920	FBXO4	106	316	5	41926160	41926370
BE073423	NUP210	3	110	3	13392813	13392920	FBXO4	102	312	5	41926160	41926370

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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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
chr5:41941351-41941351	p.L378I	2
chr5:41929935-41929935	p.E188K	2
chr5:41941379-41941379	p.R387K	1
chr5:41929976-41929976	p.E201D	1
chr5:41934278-41934278	p.N256H	1
chr5:41927273-41927273	p.K116K	1
chr5:41939669-41939669	p.F342S	1
chr5:41929858-41929858	p.G162E	1
chr5:41941382-41941382	p.*388L	1
chr5:41929978-41929978	p.E202V	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	3			7			3		3			6	4			1	1	4		5
# mutation	3			7			3		3			9	4			1	1	5		5
nonsynonymous SNV	3			6			1		1			7	4			1	1	4		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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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
chr5:41929884	p.L171L,FBXO4	2
chr5:41934414	p.R241I,FBXO4	1
chr5:41927307	p.A135V,FBXO4	1
chr5:41929974	p.R261L,FBXO4	1
chr5:41939605	p.M140L,FBXO4	1
chr5:41927319	p.F289F,FBXO4	1
chr5:41929975	p.A141T,FBXO4	1
chr5:41925578	p.K301R	1
chr5:41939628	p.S321P	1
chr5:41927329	p.N175S,FBXO4	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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