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 NEU1
Basic gene info.Gene symbolNEU1
Gene namesialidase 1 (lysosomal sialidase)
SynonymsNANH|NEU|SIAL1
CytomapUCSC genome browser: 6p21.3
Genomic locationchr6_cox_hap2 :3336575-3340456
Type of geneprotein-coding
RefGenesNM_000434.3,
Ensembl idENSG00000204386
DescriptionG9 sialidaseN-acetyl-alpha-neuraminidase 1acetylneuraminyl hydrolaseexo-alpha-sialidaselysosomal sialidasesialidase-1
Modification date20141207
dbXrefs MIM : 608272
HGNC : HGNC
Ensembl : ENSG00000204386
HPRD : 09751
Vega : OTTHUMG00000031284
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_NEU1
BioGPS: 4758
Gene Expression Atlas: ENSG00000204386
The Human Protein Atlas: ENSG00000204386
PathwayNCI Pathway Interaction Database: NEU1
KEGG: NEU1
REACTOME: NEU1
ConsensusPathDB
Pathway Commons: NEU1
MetabolismMetaCyc: NEU1
HUMANCyc: NEU1
RegulationEnsembl's Regulation: ENSG00000204386
miRBase: chr6_cox_hap2 :3,336,575-3,340,456
TargetScan: NM_000434
cisRED: ENSG00000204386
ContextiHOP: NEU1
cancer metabolism search in PubMed: NEU1
UCL Cancer Institute: NEU1
Assigned class in ccmGDBC

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Phenotypic Information for NEU1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: NEU1
Familial Cancer Database: NEU1
* 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: NEU1
MedGen: NEU1 (Human Medical Genetics with Condition)
ClinVar: NEU1
PhenotypeMGI: NEU1 (International Mouse Phenotyping Consortium)
PhenomicDB: NEU1

Mutations for NEU1
* 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 NEU1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA345305FGA1874155507732155507818NEU187215631599993160127
AI368907NEU12995631601293160195NEU193362631598263160095
BQ301319NEU19109631605813160681NEU1106273631606643161005

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=20)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr6:31829855-31829855p.L91L2
chr6:31827959-31827959p.R294H2
chr6:31829050-31829050p.D177G2
chr6:31829215-31829215p.S122F1
chr6:31830526-31830526p.L10F1
chr6:31827675-31827675p.R357W1
chr6:31828353-31828353p.G221W1
chr6:31829815-31829815p.G105W1
chr6:31830546-31830546p.G3V1
chr6:31827680-31827680p.S355L1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   102 3 1  141  63  
# mutation   102 3 1  141  64  
nonsynonymous SNV   71 1 1  131  42  
synonymous SNV   31 2     1   22  
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
chr6:31827959p.R294H2
chr6:31829855p.L91L2
chr6:31829867p.L153I1
chr6:31827680p.S355L1
chr6:31828391p.D145N1
chr6:31829870p.R294R1
chr6:31827958p.S144S1
chr6:31828967p.S122F1
chr6:31829871p.R294C1
chr6:31829050p.R280Q1

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 NEU1 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 NEU1

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

B3GALT4,BAG6,GPANK1,ABHD16A,C6orf1,C6orf47,COA3,
CUTA,FLOT1,HSD17B8,MRPS18B,NEU1,PPP1R11,NELFE,
RNF5,RNF5P1,SKIV2L,SLC39A7,VPS52,YIPF3,ZNF165
ATP6AP1,ATP6V0B,ATG101,CDK5,CLN3,COMMD5,LMAN2,
NEU1,NMRAL1,PHF23,PPP4C,SDF2,SIGIRR,SLC25A39,
SYNGR2,TEX264,TMEM141,TMEM205,TMEM54,VAMP8,VPS25

ACOT8,GID8,AAR2,RTFDC1,C6orf1,CHMP4B,CPNE1,
DYNLRB1,EDEM2,EIF6,ERGIC3,GSS,HM13,LY6G6D,
NEU1,PIGU,POFUT1,PSMA7,RALY,TP53RK,TRPC4AP
ACAA1,AMFR,APPL2,ASB13,B3GNT8,CHMP1A,FMO4,
FTH1,GPR108,IFNGR2,IL10RB,LMBRD1,MARVELD3,NAAA,
NEU1,P2RX4,PAFAH2,PNPLA1,SFXN1,SLC35D2,TPRG1L
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 NEU1
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 1 (lysosomal sialidase)approvedOseltamivir


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Cross referenced IDs for NEU1
* 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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