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 NUDT12
Basic gene info.Gene symbolNUDT12
Gene namenudix (nucleoside diphosphate linked moiety X)-type motif 12
Synonyms-
CytomapUCSC genome browser: 5q21.2
Genomic locationchr5 :102884555-102898490
Type of geneprotein-coding
RefGenesNM_001300741.1,
NM_031438.3,
Ensembl idENSG00000112874
Descriptionnucleoside diphosphate linked moiety X-type motif 12nucleoside diphosphate-linked moiety X motif 12nudix motif 12peroxisomal NADH pyrophosphatase NUDT12
Modification date20141207
dbXrefs MIM : 609232
HGNC : HGNC
Ensembl : ENSG00000112874
HPRD : 10123
Vega : OTTHUMG00000128739
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NUDT12
BioGPS: 83594
Gene Expression Atlas: ENSG00000112874
The Human Protein Atlas: ENSG00000112874
PathwayNCI Pathway Interaction Database: NUDT12
KEGG: NUDT12
REACTOME: NUDT12
ConsensusPathDB
Pathway Commons: NUDT12
MetabolismMetaCyc: NUDT12
HUMANCyc: NUDT12
RegulationEnsembl's Regulation: ENSG00000112874
miRBase: chr5 :102,884,555-102,898,490
TargetScan: NM_001300741
cisRED: ENSG00000112874
ContextiHOP: NUDT12
cancer metabolism search in PubMed: NUDT12
UCL Cancer Institute: NUDT12
Assigned class in ccmGDBC

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Phenotypic Information for NUDT12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NUDT12
Familial Cancer Database: NUDT12
* 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_NICOTINATE_AND_NICOTINAMIDE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NUDT12
MedGen: NUDT12 (Human Medical Genetics with Condition)
ClinVar: NUDT12
PhenotypeMGI: NUDT12 (International Mouse Phenotyping Consortium)
PhenomicDB: NUDT12

Mutations for NUDT12
* 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 NUDT12 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
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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=29)
Stat. for Synonymous SNVs
(# total SNVs=8)
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
chr5:102894933-102894933p.T148I3
chr5:102894586-102894586p.E264Q2
chr5:102894709-102894709p.G223*2
chr5:102891660-102891660p.G312G2
chr5:102886569-102886569p.N461I2
chr5:102891756-102891756p.R280R2
chr5:102891757-102891757p.R280Q2
chr5:102891788-102891788p.Q270*1
chr5:102895015-102895015p.F121L1
chr5:102886665-102886665p.D429G1

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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
# sample1  41 4 2  21   1516
# mutation1  41 4 2  21   1516
nonsynonymous SNV1  31 3 1  21   1414
synonymous SNV   1  1 1        1 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
chr5:102891660p.G312G2
chr5:102895167p.P158S1
chr5:102887996p.C400C1
chr5:102891795p.F150L1
chr5:102895744p.E358K1
chr5:102890447p.F121L1
chr5:102894586p.F356C1
chr5:102895751p.L97F1
chr5:102890452p.A354T1
chr5:102894605p.D84A1

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 NUDT12 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 NUDT12

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

ANKRA2,CSNK1G3,DCTN4,FAM114A2,FBXL17,FBXL5,FNIP1,
FOXA1,GIN1,NDFIP1,NUDT12,PGGT1B,PJA2,POLK,
RAD17,RAD50,SCAMP1,TMED7,TMEM161B,TRIM23,YTHDC2
ANGEL2,CBR4,CD2AP,DTWD2,GPD2,IKZF5,KLHL28,
METTL15,MIER3,MOB1B,MPP5,NUDT12,NUPL1,RAD1,
SLC30A9,THAP5,TRIM33,TRUB1,ZBTB41,ZNF24,ZNF680

ACN9,ANKRA2,C3orf38,C4orf33,C5orf30,TRAPPC13,C6orf57,
CAPZA2,COMMD10,CRBN,DERA,FPGT,HIGD1A,MAT2B,
MRPS36,NUDT12,RNF14,SAMD13,SKP1,SLC25A46,ZCCHC10
ATG5,SFR1,C18orf32,C6orf211,CTDSPL2,EBAG9,FPGT,
NDUFB5,NUDT12,NXT2,OCIAD1,ORC4,RNF14,SCOC,
SDHD,SRP9,TGDS,TM2D1,TMEM106B,TMEM68,TWF1
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 NUDT12


There's no related Drug.
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Cross referenced IDs for NUDT12
* 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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