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 FMO5
Basic gene info.Gene symbolFMO5
Gene nameflavin containing monooxygenase 5
Synonyms-
CytomapUCSC genome browser: 1q21.1
Genomic locationchr1 :146657837-146697230
Type of geneprotein-coding
RefGenesNM_001144829.2,
NM_001144830.2,NM_001461.3,
Ensembl idENSG00000266748
DescriptionFMO 5dimethylaniline monooxygenase [N-oxide-forming] 5dimethylaniline oxidase 5hepatic flavin-containing monooxygenase 5
Modification date20141207
dbXrefs MIM : 603957
HGNC : HGNC
Ensembl : ENSG00000131781
HPRD : 04904
Vega : OTTHUMG00000014607
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_FMO5
BioGPS: 2330
Gene Expression Atlas: ENSG00000266748
The Human Protein Atlas: ENSG00000266748
PathwayNCI Pathway Interaction Database: FMO5
KEGG: FMO5
REACTOME: FMO5
ConsensusPathDB
Pathway Commons: FMO5
MetabolismMetaCyc: FMO5
HUMANCyc: FMO5
RegulationEnsembl's Regulation: ENSG00000266748
miRBase: chr1 :146,657,837-146,697,230
TargetScan: NM_001144829
cisRED: ENSG00000266748
ContextiHOP: FMO5
cancer metabolism search in PubMed: FMO5
UCL Cancer Institute: FMO5
Assigned class in ccmGDBC

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Phenotypic Information for FMO5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: FMO5
Familial Cancer Database: FMO5
* 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: FMO5
MedGen: FMO5 (Human Medical Genetics with Condition)
ClinVar: FMO5
PhenotypeMGI: FMO5 (International Mouse Phenotyping Consortium)
PhenomicDB: FMO5

Mutations for FMO5
* 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 FMO5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA491849FMO581071146656768146656867FMO51052781146656863146657036
AI240595MPPE11469181188405411884109FMO5653771146676325146676637
AW972276FMO51112101146656768146656867FMO52083811146656863146657036

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        2    1   
GAIN (# sample)        2    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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=49)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=1)
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
chr1:146673058-146673058p.D287N3
chr1:146672890-146672890p.V343I2
chr1:146683995-146683995p.D199G2
chr1:146658627-146658627p.R485Q2
chr1:146683996-146683996p.D199H2
chr1:146672824-146672824p.T365P2
chr1:146684893-146684893p.P157S1
chr1:146687424-146687424p.I75N1
chr1:146673057-146673057p.D287G1
chr1:146658804-146658804p.H426R1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample32114    3  343  95 8
# mutation42113    3  343  96 8
nonsynonymous SNV32111    2  323  76 6
synonymous SNV1  2    1   2   2  2
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
chr1:146673058p.D287Y,FMO53
chr1:146656151p.D439N2
chr1:146673043p.T365P,FMO52
chr1:146672824p.R292S,FMO52
chr1:146672922p.V88G,FMO51
chr1:146680526p.F393C,FMO51
chr1:146658801p.R277G,FMO51
chr1:146685000p.I261T,FMO51
chr1:146672930p.S64F,FMO51
chr1:146680607p.V392G,FMO51

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 FMO5 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 FMO5

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

ALDH6A1,BTD,C1orf21,C1orf27,CD46,COG2,CYB5D1,
EDEM3,ESR1,FMO5,IQGAP2,KIAA0040,KIF13B,LRIG1,
OTUD7B,RABEP1,RALGPS2,TMEM144,TOR1AIP1,ZBTB41,ZCWPW2
ABCC12,ACSL3,ADCY10,C15orf43,CCDC15,CTNNA2,EPS8L3,
FMO5,HIST1H2AG,HMGCS2,IDI1,IYD,LST-3TM12,PON3,
PXMP4,RNASE12,SERHL,SGPP2,SLC12A3,TMEM62,TMPRSS11F

AOC1,APPL2,BCAS1,C11orf86,C1orf210,C1orf94,CDHR5,
CLDN23,DHRS9,FMO5,GDPD2,LOC646627,MMP28,MYPN,
PLA2G10,RNF103,SMPDL3A,TSPAN1,UGT1A4,UGT1A5,VSIG1
ADPRHL1,ASTE1,C11orf52,CES2,CYP2S1,FMO5,GUCY2C,
HSD17B11,MEP1A,NGEF,PIWIL2,PMM1,RAB17,RNF128,
SLC39A5,STRADB,TMBIM6,TMEM120A,TNNC2,USH1C,VSIG10
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 FMO5


There's no related Drug.
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Cross referenced IDs for FMO5
* 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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