Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

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 symbol	NEU1
	Gene name	sialidase 1 (lysosomal sialidase)
	Synonyms	NANH\|NEU\|SIAL1
	Cytomap	UCSC genome browser: 6p21.3
	Genomic location	chr6_cox_hap2 :3336575-3340456
	Type of gene	protein-coding
	RefGenes	NM_000434.3,
	Ensembl id	ENSG00000204386
	Description	G9 sialidaseN-acetyl-alpha-neuraminidase 1acetylneuraminyl hydrolaseexo-alpha-sialidaselysosomal sialidasesialidase-1
	Modification date	20141207
dbXrefs	MIM : 608272
	HGNC : HGNC
	Ensembl : ENSG00000204386
	HPRD : 09751
	Vega : OTTHUMG00000031284
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_NEU1
	BioGPS: 4758
	Gene Expression Atlas: ENSG00000204386
	The Human Protein Atlas: ENSG00000204386
Pathway	NCI Pathway Interaction Database: NEU1
	KEGG: NEU1
	REACTOME: NEU1
	ConsensusPathDB
	Pathway Commons: NEU1
Metabolism	MetaCyc: NEU1
	HUMANCyc: NEU1
Regulation	Ensembl's Regulation: ENSG00000204386
	miRBase: chr6_cox_hap2 :3,336,575-3,340,456
	TargetScan: NM_000434
	cisRED: ENSG00000204386
Context	iHOP: NEU1
	cancer metabolism search in PubMed: NEU1
	UCL Cancer Institute: NEU1
Assigned class in ccmGDB	C

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Phenotypic Information for NEU1(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
KEGG_SPHINGOLIPID_METABOLISM REACTOME_GLYCOSPHINGOLIPID_METABOLISM REACTOME_PHOSPHOLIPID_METABOLISM REACTOME_SPHINGOLIPID_METABOLISM REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: NEU1
	MedGen: NEU1 (Human Medical Genetics with Condition)
	ClinVar: NEU1
Phenotype	MGI: NEU1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows NEU1 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
AA345305	FGA	1	87	4	155507732	155507818	NEU1	87	215	6	3159999	3160127
AI368907	NEU1	29	95	6	3160129	3160195	NEU1	93	362	6	3159826	3160095
BQ301319	NEU1	9	109	6	3160581	3160681	NEU1	106	273	6	3160664	3161005

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr6:31827959-31827959	p.R294H	2
chr6:31829050-31829050	p.D177G	2
chr6:31829855-31829855	p.L91L	2
chr6:31828374-31828374	p.R214C	1
chr6:31829867-31829867	p.R87R	1
chr6:31827913-31827913	p.F309F	1
chr6:31828967-31828967	p.Q205K	1
chr6:31829868-31829868	p.R87Q	1
chr6:31827958-31827958	p.R294R	1
chr6:31829027-31829027	p.R185G	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample				10	2		3		1			1	4	1			6	3
# mutation				10	2		3		1			1	4	1			6	4
nonsynonymous SNV				7	1		1		1			1	3	1			4	2
synonymous SNV				3	1		2						1				2	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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr6:31829855	p.R294H	2
chr6:31827959	p.L91L	2
chr6:31829050	p.P86P	1
chr6:31829904	p.C265C	1
chr6:31827960	p.P86L	1
chr6:31829061	p.Y251Y	1
chr6:31829926	p.D75G	1
chr6:31828001	p.G221W	1
chr6:31829067	p.G219D	1
chr6:31830506	p.G68R	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00198	sialidase 1 (lysosomal sialidase)	approved	Oseltamivir

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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