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 NEU2
Basic gene info.Gene symbolNEU2
Gene namesialidase 2 (cytosolic sialidase)
SynonymsSIAL2
CytomapUCSC genome browser: 2q37
Genomic locationchr2 :233897381-233899767
Type of geneprotein-coding
RefGenesNM_005383.2,
Ensembl idENSG00000115488
DescriptionN-acetyl-alpha-neuraminidase 2cytosolic sialidaseneuraminidase 2sialidase-2
Modification date20141207
dbXrefs MIM : 605528
HGNC : HGNC
Ensembl : ENSG00000115488
HPRD : 05702
Vega : OTTHUMG00000133274
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NEU2
BioGPS: 4759
Gene Expression Atlas: ENSG00000115488
The Human Protein Atlas: ENSG00000115488
PathwayNCI Pathway Interaction Database: NEU2
KEGG: NEU2
REACTOME: NEU2
ConsensusPathDB
Pathway Commons: NEU2
MetabolismMetaCyc: NEU2
HUMANCyc: NEU2
RegulationEnsembl's Regulation: ENSG00000115488
miRBase: chr2 :233,897,381-233,899,767
TargetScan: NM_005383
cisRED: ENSG00000115488
ContextiHOP: NEU2
cancer metabolism search in PubMed: NEU2
UCL Cancer Institute: NEU2
Assigned class in ccmGDBC

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Phenotypic Information for NEU2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NEU2
Familial Cancer Database: NEU2
* 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_SPHINGOLIPID_METABOLISM
REACTOME_GLYCOSPHINGOLIPID_METABOLISM
REACTOME_PHOSPHOLIPID_METABOLISM
REACTOME_SPHINGOLIPID_METABOLISM
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: NEU2
MedGen: NEU2 (Human Medical Genetics with Condition)
ClinVar: NEU2
PhenotypeMGI: NEU2 (International Mouse Phenotyping Consortium)
PhenomicDB: NEU2

Mutations for NEU2
* 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 NEU2 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=3

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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=19)
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
chr2:233899691-233899691p.A356V2
chr2:233899362-233899362p.A246A2
chr2:233899563-233899563p.P313P2
chr2:233899564-233899564p.R314*2
chr2:233897493-233897493p.A38T2
chr2:233899574-233899574p.A317V2
chr2:233899725-233899725p.F367F2
chr2:233897503-233897503p.R41Q2
chr2:233899290-233899290p.A222A2
chr2:233899687-233899687p.E355K2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1 262 2    94   116 4
# mutation1 272 2    94   156 6
nonsynonymous SNV1 152      32   113 3
synonymous SNV  12  2    62   43 3
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
chr2:233899574p.A38T2
chr2:233897493p.P313P2
chr2:233899563p.A317V2
chr2:233897387p.P5S1
chr2:233899356p.L124M1
chr2:233898898p.A246A1
chr2:233899109p.E355K1
chr2:233897394p.L7L1
chr2:233899362p.T135T1
chr2:233898903p.Q270H1

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 NEU2 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 NEU2

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

DUSP7,GK2,IFNK,IL1A,IVL,KLK9,KRT6A,
NEU2,OR2T2,OR51A4,OR51L1,OR5AP2,OR5L2,OR8H3,
REG1P,SBSN,SDR9C7,SFN,SPINK7,SPRR1B,TAAR2
ACTL6B,CARTPT,CPLX2,EPYC,AMER3,FLJ36000,GIP,
HMP19,IBSP,IFNA14,LCE2D,LOC650293,LOC729121,LOC732275,
NEU2,OR8B2,OR8H3,PCSK1,SEZ6,SYT4,TRIM48

BMP5,DLX6AS,EDNRA,ERP27,EYS,HAVCR1,HIST1H2BA,
KCTD16,KRT36,KRT38,LOC374491,MYL3,NAV2,NEU2,
OR10S1,OR6M1,PDE3A,RPS6KC1,SEMA5A,UGT2A3,UNC13C
ART1,BTBD6,TBATA,CHAD,FAM163B,FAM19A1,FRG2C,
GPRIN2,HTR7,IL37,KRTAP5-7,LOC338651,MNX1,NEU2,
NOBOX,PCK1,PROC,QPRT,SLC44A5,SOX14,SPINK7
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 NEU2
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
DB00198sialidase 2 (cytosolic sialidase)approvedOseltamivir
DB00558sialidase 2 (cytosolic sialidase)approved; investigationalZanamivir
DB03991sialidase 2 (cytosolic sialidase)experimental2-Deoxy-2,3-Dehydro-N-Acetyl-Neuraminic Acid
DB07960sialidase 2 (cytosolic sialidase)experimental5-ACETAMIDO-5,6-DIHYDRO-4-HYDROXY-6-ISOBUTOXY-4H-PYRAN-2-CARBOXYLIC ACID


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Cross referenced IDs for NEU2
* 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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