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 NIT2
Basic gene info.Gene symbolNIT2
Gene namenitrilase family, member 2
SynonymsHEL-S-8a
CytomapUCSC genome browser: 3q12.2
Genomic locationchr3 :100053561-100074478
Type of geneprotein-coding
RefGenesNM_020202.4,
Ensembl idENSG00000114021
DescriptionNit protein 2epididymis secretory sperm binding protein Li 8anitrilase homolog 2omega-amidase NIT2
Modification date20141207
dbXrefs HGNC : HGNC
HPRD : 17634
ProteinUniProt: Q9NQR4
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NIT2
BioGPS: 56954
Gene Expression Atlas: ENSG00000114021
The Human Protein Atlas: ENSG00000114021
PathwayNCI Pathway Interaction Database: NIT2
KEGG: NIT2
REACTOME: NIT2
ConsensusPathDB
Pathway Commons: NIT2
MetabolismMetaCyc: NIT2
HUMANCyc: NIT2
RegulationEnsembl's Regulation: ENSG00000114021
miRBase: chr3 :100,053,561-100,074,478
TargetScan: NM_020202
cisRED: ENSG00000114021
ContextiHOP: NIT2
cancer metabolism search in PubMed: NIT2
UCL Cancer Institute: NIT2
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of NIT2 in cancer cell metabolism1. Krasnikov BF, Chien C-H, Nostramo R, Pinto JT, Nieves E, et al. (2009) Identification of the putative tumor suppressor Nit2 as ω-amidase, an enzyme metabolically linked to glutamine and asparagine transamination. Biochimie 91: 1072-1080. go to article
2. Chien C-H, Gao Q-Z, Cooper AJ, Lyu J-H, Sheu S-Y (2012) Structural Insights into the Catalytic Active Site and Activity of Human Nit2/ω-Amidase KINETIC ASSAY AND MOLECULAR DYNAMICS SIMULATION. Journal of Biological Chemistry 287: 25715-25726. go to article

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Phenotypic Information for NIT2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NIT2
Familial Cancer Database: NIT2
* 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_ALANINE_ASPARTATE_AND_GLUTAMATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NIT2
MedGen: NIT2 (Human Medical Genetics with Condition)
ClinVar: NIT2
PhenotypeMGI: NIT2 (International Mouse Phenotyping Consortium)
PhenomicDB: NIT2

Mutations for NIT2
* 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 NIT2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample2                
GAIN (# sample)2                
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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=23)
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
chr3:100064474-100064474p.E128*3
chr3:100065064-100065064p.R157Q2
chr3:100057936-100057936p.R5C2
chr3:100058688-100058688p.K52K2
chr3:100064520-100064520p.T143I1
chr3:100057981-100057981p.N20D1
chr3:100071315-100071315p.A218S1
chr3:100058731-100058731p.Q67*1
chr3:100074111-100074111p.*277*1
chr3:100064522-100064522p.P144S1

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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
# sample 1 31   3  222  13 4
# mutation 1 31   4  222  13 4
nonsynonymous SNV   31   3   12  12 3
synonymous SNV 1      1  21    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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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
chr3:100065064p.R157Q2
chr3:100058042p.S40Y2
chr3:100058021p.A51A1
chr3:100058029p.R255H1
chr3:100065092p.I61V1
chr3:100067652p.L80V1
chr3:100058049p.L80L1
chr3:100067663p.G83V1
chr3:100058685p.G83G1
chr3:100067690p.E128K1

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 NIT2 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 NIT2

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

ALG3,TIMMDC1,CMSS1,CCDC58,CHCHD6,COX17,COX7B,
DPY30,MRPL22,NDUFA1,NDUFB4,NIT2,POLR2H,TRMT10C,
RNF7,RPL24,RUVBL1,TFG,TPRA1,TXNDC17,USMG5
ACSM2B,AMN,APOC3,BMP3,TBATA,IZUMO4,DCXR,
EIF4EBP1,GCDH,MPST,NIT2,PCBD1,PCYT2,PDZD7,
PMM1,PXMP2,SNORA14A,ST8SIA3,TH,TMEM120A,TTC36

AHCY,ATP5J2,CMSS1,MPLKIP,MALSU1,CHCHD2,CHCHD6,
CMC1,DNAJC19,LOC440957,MRPL3,MRPL48,MRPS33,NHP2,
NIT2,TRMT10C,ROMO1,RPL24,RPS21,SSBP1,THOC7
ACN9,DTD2,C1QBP,TMEM261,CCNC,DCTPP1,MRPL11,
MRPL32,MRPS22,MRPS28,MRPS35,NIT2,NME2,RPS18,
RPS6,TAF9,TMEM14B,TOMM22,TOMM6,UQCRH,WDR61
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 NIT2


There's no related Drug.
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Cross referenced IDs for NIT2
* 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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