Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 NFS1
Basic gene info.Gene symbolNFS1
Gene nameNFS1 cysteine desulfurase
SynonymsIscS|NIFS
CytomapUCSC genome browser: 20q11.22
Genomic locationchr20 :34256609-34287287
Type of geneprotein-coding
RefGenesNM_001198989.1,
NM_021100.4,NR_037570.2,NM_181679.1,
Ensembl idENSG00000244005
DescriptionNFS1 nitrogen fixation 1 homologcysteine desulfurase, mitochondrialnitrogen fixation 1 (S. cerevisiae, homolog)nitrogen-fixing bacteria S-like protein
Modification date20141207
dbXrefs MIM : 603485
HGNC : HGNC
Ensembl : ENSG00000244005
HPRD : 04597
Vega : OTTHUMG00000032361
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NFS1
BioGPS: 9054
Gene Expression Atlas: ENSG00000244005
The Human Protein Atlas: ENSG00000244005
PathwayNCI Pathway Interaction Database: NFS1
KEGG: NFS1
REACTOME: NFS1
ConsensusPathDB
Pathway Commons: NFS1
MetabolismMetaCyc: NFS1
HUMANCyc: NFS1
RegulationEnsembl's Regulation: ENSG00000244005
miRBase: chr20 :34,256,609-34,287,287
TargetScan: NM_001198989
cisRED: ENSG00000244005
ContextiHOP: NFS1
cancer metabolism search in PubMed: NFS1
UCL Cancer Institute: NFS1
Assigned class in ccmGDBC

Top
Phenotypic Information for NFS1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NFS1
Familial Cancer Database: NFS1
* 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_VITAMINS_AND_COFACTORS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NFS1
MedGen: NFS1 (Human Medical Genetics with Condition)
ClinVar: NFS1
PhenotypeMGI: NFS1 (International Mouse Phenotyping Consortium)
PhenomicDB: NFS1

Mutations for NFS1
* 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
haematopoietic_and_lymphoid_tissueNFS1chr203426576434265764NFS1chr203426576434265764
ovaryNFS1chr203425682934256849chr12696796126967981
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 NFS1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DW417230NFS117107203427682934276919HGD1061343120389826120389861

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2     1 1        
GAIN (# sample)2     1 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)

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=33)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr20:34262318-34262318p.E364K2
chr20:34263099-34263099p.R272R2
chr20:34260686-34260686p.R434Q2
chr20:34268668-34268668p.G261S1
chr20:34260738-34260738p.E417Q1
chr20:34278354-34278354p.S181I1
chr20:34262520-34262520p.S323*1
chr20:34285655-34285655p.T92I1
chr20:34268676-34268676p.K258R1
chr20:34260741-34260741p.E416Q1

Top
check002.gifSNV 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 ID1234567891011121314151617181920
# sample2216  1 4  63   42 4
# mutation2216  1 4  63   42 6
nonsynonymous SNV21 6  1 3  53   21 5
synonymous SNV 11     1  1    21 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])

Top
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
chr20:34278343p.K320K,NFS11
chr20:34261595p.V176A,NFS11
chr20:34286483p.G34E,NFS11
chr20:34263075p.V310M,NFS11
chr20:34278354p.I167L,NFS11
chr20:34262293p.I279V,NFS11
chr20:34286486p.L186I1
chr20:34263091p.R277R,NFS11
chr20:34278366p.D185Y1
chr20:34262295p.I271I,NFS11

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 NFS1 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]

Top
Gene Expression for NFS1

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

C20orf24,AAR2,CEP250,CPNE1,DSN1,DYNLRB1,EDEM2,
EIF6,ERGIC3,GSS,LOC647979,MOCS3,NCOA6,NDRG3,
NFS1,PHF20,PIGU,RBM39,ROMO1,TRPC4AP,UQCC1
ATP5A1,C21orf33,CLYBL,COQ6,CPT2,CYC1,DNAJA3,
ERAL1,HAX1,HSPA9,IDH3B,MRPL37,MRPL44,MRPS18B,
MRPS7,NDUFA10,NFS1,SNRNP25,TACO1,TSFM,TXN2

ACTR5,AAR2,CDK5RAP1,CPNE1,CTNNBL1,DDX27,DHX35,
EIF2S2,EIF6,GSS,MTG2,TTI1,NFS1,PIGU,
POFUT1,RALY,NELFCD,TM9SF4,TRPC4AP,UBE2V1,UQCC1
ADH1C,ADH6,DDAH1,EHHADH,FAM117B,HMGCS2,HOXB6,
HOXB8,KIFAP3,LRPPRC,NAALADL2,NDUFA10,NFS1,PAQR5,
PCCA,SATL1,SH2D4A,SIRT5,SLC19A1,SLC38A4,SUCLG2
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for NFS1
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
DB00114NFS1 nitrogen fixation 1 homolog (S. cerevisiae)nutraceuticalPyridoxal Phosphate
DB00151NFS1 nitrogen fixation 1 homolog (S. cerevisiae)approved; nutraceuticalL-Cysteine
DB00160NFS1 nitrogen fixation 1 homolog (S. cerevisiae)approved; nutraceuticalL-Alanine


Top
Cross referenced IDs for NFS1
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas