Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 FMO4
Basic gene info.Gene symbolFMO4
Gene nameflavin containing monooxygenase 4
SynonymsFMO2
CytomapUCSC genome browser: 1q24.3
Genomic locationchr1 :171283485-171311223
Type of geneprotein-coding
RefGenesNM_002022.1,
Ensembl idENSG00000076258
DescriptionFMO 4dimethylaniline monooxygenase [N-oxide-forming] 4dimethylaniline oxidase 4hepatic flavin-containing monooxygenase 4
Modification date20141207
dbXrefs MIM : 136131
HGNC : HGNC
Ensembl : ENSG00000076258
HPRD : 00632
Vega : OTTHUMG00000035506
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FMO4
BioGPS: 2329
Gene Expression Atlas: ENSG00000076258
The Human Protein Atlas: ENSG00000076258
PathwayNCI Pathway Interaction Database: FMO4
KEGG: FMO4
REACTOME: FMO4
ConsensusPathDB
Pathway Commons: FMO4
MetabolismMetaCyc: FMO4
HUMANCyc: FMO4
RegulationEnsembl's Regulation: ENSG00000076258
miRBase: chr1 :171,283,485-171,311,223
TargetScan: NM_002022
cisRED: ENSG00000076258
ContextiHOP: FMO4
cancer metabolism search in PubMed: FMO4
UCL Cancer Institute: FMO4
Assigned class in ccmGDBC

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Phenotypic Information for FMO4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FMO4
Familial Cancer Database: FMO4
* 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
KEGG_DRUG_METABOLISM_CYTOCHROME_P450

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: FMO4
MedGen: FMO4 (Human Medical Genetics with Condition)
ClinVar: FMO4
PhenotypeMGI: FMO4 (International Mouse Phenotyping Consortium)
PhenomicDB: FMO4

Mutations for FMO4
* 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 FMO4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI010334HECA204246139501266139501673FMO44155941171308728171308908

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=59)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr1:171303694-171303694p.V324V2
chr1:171300821-171300821p.Y176C2
chr1:171303720-171303720p.S333Y2
chr1:171301933-171301933p.R238K2
chr1:171303754-171303754p.L344L2
chr1:171293385-171293385p.M144V2
chr1:171310800-171310800p.R500Q2
chr1:171300796-171300796p.G168C1
chr1:171303684-171303684p.I321T1
chr1:171310826-171310826p.A509T1

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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
# sample32 11  4  1 641  84 10
# mutation52 10  4  1 651  84 10
nonsynonymous SNV42 9  4  1 34   73 7
synonymous SNV1  1       311  11 3
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
chr1:171303720p.S333F3
chr1:171310800p.E130K2
chr1:171293343p.R500Q2
chr1:171301933p.L344L2
chr1:171303754p.R238K2
chr1:171303645p.I273V1
chr1:171293307p.D435Y1
chr1:171303865p.E132D1
chr1:171300851p.V302M1
chr1:171303659p.I437I1

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 FMO4 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 FMO4

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

ADAM7,ANKRD34C,C12orf74,C16orf62,CASP8,CLCA2,FABP6,
FMO1,FMO4,KYNU,LITAF,MAGEC1,MPV17L,MYLK3,
OR52E6,PLEKHG7,PRR23A,TBC1D24,TMC5,TMC7,TOP1P1
ATMIN,ATP2C1,CCDC170,CTSO,DYNC2H1,FCF1,FMO4,
MYO1B,NEK11,PLD1,PLEKHA5,RBM43,SCARB2,SERPINI1,
SPRED2,SPTLC3,SRBD1,TCTN3,TERF1,TM7SF3,ZFP90

ABCC5,CARF,C7orf31,CCDC159,CXorf23,FCHSD1,FMO4,
GTF2IRD2P1,ILDR1,KCTD18,KIAA1407,LOC375190,NUDT7,OR2A9P,
PARK2,PBLD,PHYH,TTC14,ZC4H2,ZNF19,ZNF846
ACVR2A,ANO10,LRRC75A,C1orf106,C1orf115,COL17A1,DHRS11,
FMO4,GCOM1,GDPD2,KCNK5,KIAA0247,MAST2,MGAT4A,
NR1I2,PBLD,SCIN,SEPHS2,SLC9A3R1,SPINT1,TMEM82
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 FMO4
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00763flavin containing monooxygenase 4approvedMethimazole


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Cross referenced IDs for FMO4
* 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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