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 NANP
Basic gene info.Gene symbolNANP
Gene nameN-acetylneuraminic acid phosphatase
SynonymsC20orf147|HDHD4|dJ694B14.3
CytomapUCSC genome browser: 20p11.1
Genomic locationchr20 :25593572-25604648
Type of geneprotein-coding
RefGenesNM_152667.2,
Ensembl idENSG00000170191
DescriptionN-acylneuraminate-9-phosphataseNeu5Ac-9-Pasehaloacid dehalogenase-like hydrolase domain containing 4haloacid dehalogenase-like hydrolase domain-containing protein 4
Modification date20141207
dbXrefs MIM : 610763
HGNC : HGNC
Ensembl : ENSG00000170191
HPRD : 17097
Vega : OTTHUMG00000032132
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NANP
BioGPS: 140838
Gene Expression Atlas: ENSG00000170191
The Human Protein Atlas: ENSG00000170191
PathwayNCI Pathway Interaction Database: NANP
KEGG: NANP
REACTOME: NANP
ConsensusPathDB
Pathway Commons: NANP
MetabolismMetaCyc: NANP
HUMANCyc: NANP
RegulationEnsembl's Regulation: ENSG00000170191
miRBase: chr20 :25,593,572-25,604,648
TargetScan: NM_152667
cisRED: ENSG00000170191
ContextiHOP: NANP
cancer metabolism search in PubMed: NANP
UCL Cancer Institute: NANP
Assigned class in ccmGDBC

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

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

Mutations for NANP
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
central_nervous_systemNANPchr202559562125595621chr171580779615807796
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 NANP 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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr20:25597039-25597039p.R90T2
chr20:25596776-25596776p.G178R2
chr20:25596915-25596915p.T131T1
chr20:25596916-25596916p.T131M1
chr20:25596953-25596953p.T119A1
chr20:25596977-25596977p.A111S1
chr20:25597014-25597014p.F98F1
chr20:25597030-25597030p.A93G1
chr20:25596622-25596622p.S229F1
chr20:25596634-25596634p.Y225C1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1  1 2    31   12 2
# mutation 1  1 2    31   12 2
nonsynonymous SNV 1  1 1    2     1 1
synonymous SNV      1    11   11 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
chr20:25596915p.A93G1
chr20:25596977p.A87P1
chr20:25597030p.A79G1
chr20:25597049p.Q36Q1
chr20:25597072p.M28K1
chr20:25597200p.I18I1
chr20:25596639p.P223P1
chr20:25604502p.N212N1
chr20:25596672p.T206T1
chr20:25604531p.G178R1

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 NANP 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 NANP

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

MGME1,CENPI,CHEK1,DBF4,DLGAP5,ERCC6L,ESF1,
GINS1,GMPS,KIF18A,MAPRE1,MCM8,NANP,PCNA,
PNPT1,POLR3F,RBBP9,STIL,SUV39H2,TPX2,TRMT6
ATP6AP2,C3orf38,CAPZA1,GOLT1B,GRPEL2,KCTD6,NANP,
NDFIP1,PDCD10,PLEKHA3,RAB22A,RBM7,SREK1IP1,SSR1,
CNEP1R1,TMX1,TRAM1,TXNDC9,VMA21,YIPF5,ZNF684

ABHD12,APMAP,AAR2,CRNKL1,CSTF1,CTNNBL1,DSN1,
ENTPD6,GINS1,ITCH,MAPRE1,NAA20,NANP,NXT1,
PIGU,POLR3F,RPRD1B,NELFCD,XRN2,YTHDF1,ZNF337
FAM204A,AAED1,COPS3,COPS8,CTNNAL1,DIMT1,DNAJC8,
GLO1,LSM10,MOCS2,MORF4L2,MTMR6,NANP,BBIP1,
NMD3,PEX3,PRKRA,RNF115,RWDD1,UBA2,UTP11L
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 NANP


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