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

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 ST8SIA3

Basic gene info.	Gene symbol	ST8SIA3
	Gene name	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 3
	Synonyms	SIAT8C\|ST8SiaIII
	Cytomap	UCSC genome browser: 18q21.31
	Genomic location	chr18 :55019720-55036161
	Type of gene	protein-coding
	RefGenes	NM_015879.2,
	Ensembl id	ENSG00000177511
	Description	SIAT8-Calpha-2,8-sialyltransferase 8Calpha-2,8-sialyltransferase IIIsia-alpha-2,3-Gal-beta-1,4-GlcNAc-R:alpha 2,8-sialyltransferasesialyltransferase 8C (alpha2,3Galbeta1,4GlcNAcalpha 2,8-sialyltransferase)sialyltransferase St8Sia IIIsialytransferase
	Modification date	20141207
dbXrefs	MIM : 609478
	HGNC : HGNC
	Ensembl : ENSG00000177511
	HPRD : 15343
	Vega : OTTHUMG00000180101
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ST8SIA3
	BioGPS: 51046
	Gene Expression Atlas: ENSG00000177511
	The Human Protein Atlas: ENSG00000177511
Pathway	NCI Pathway Interaction Database: ST8SIA3
	KEGG: ST8SIA3
	REACTOME: ST8SIA3
	ConsensusPathDB
	Pathway Commons: ST8SIA3
Metabolism	MetaCyc: ST8SIA3
	HUMANCyc: ST8SIA3
Regulation	Ensembl's Regulation: ENSG00000177511
	miRBase: chr18 :55,019,720-55,036,161
	TargetScan: NM_015879
	cisRED: ENSG00000177511
Context	iHOP: ST8SIA3
	cancer metabolism search in PubMed: ST8SIA3
	UCL Cancer Institute: ST8SIA3
Assigned class in ccmGDB	C

Top

Phenotypic Information for ST8SIA3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ST8SIA3
	Familial Cancer Database: ST8SIA3

* 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
REACTOME_METABOLISM_OF_PROTEINS

Others
OMIM
Orphanet
Disease	KEGG Disease: ST8SIA3
	MedGen: ST8SIA3 (Human Medical Genetics with Condition)
	ClinVar: ST8SIA3
Phenotype	MGI: ST8SIA3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ST8SIA3

Mutations for ST8SIA3

* 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 ST8SIA3 related fusion information.

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

CA773823

ST8SIA3

278

55030334

55030607

ST8SIA3

274

347

55028520

55028593

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

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

Top

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=5

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=50)	Stat. for Synonymous SNVs (# total SNVs=22)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr18:55024414-55024414	p.F191F	5
chr18:55024154-55024154	p.L105I	3
chr18:55024677-55024677	p.G279E	3
chr18:55021743-55021743	p.F97C	3
chr18:55024534-55024534	p.F231L	2
chr18:55024348-55024348	p.G169G	2
chr18:55024537-55024537	p.F232F	2
chr18:55024403-55024403	p.R188C	2
chr18:55024205-55024205	p.R122W	2
chr18:55027323-55027323	p.G320R	2

Top

SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	2	1	13	1		2		2			8	8			1	18	3		7
# mutation	1	2	1	15	1		2		2			8	10			1	20	2		10
nonsynonymous SNV	1	1	1	13			2		1			8	3			1	14	2		8
synonymous SNV		1		2	1				1				7				6			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])

Top

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
chr18:55027323	p.A21T	2
chr18:55020138	p.G279E	2
chr18:55021743	p.E216K	2
chr18:55024487	p.G320R	2
chr18:55024677	p.F97C	2
chr18:55024414	p.F191F	2
chr18:55020133	p.D109N	1
chr18:55024415	p.E195K	1
chr18:55027470	p.T372N	1
chr18:55021644	p.L23L	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 ST8SIA3 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]

Top

Gene Expression for ST8SIA3

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


CACNG5,CBLN1,FEV,GAD2,GDNF,INSRR,KCNH3, KRTAP27-1,MEP1B,NEUROD1,NRSN1,OR4P4,PIWIL1,RALYL, SAMD14,SNCB,SNTG1,ST8SIA3,SYNGR4,TRPM3,WNT16	ACSM2A,ACSM2B,AMN,APOC3,APOL4,TBATA,CHGA, CHGB,CPO,DBH,NDRG4,NTSR2,ORM1,ORM2, PDZD7,PHOX2B,SLC18A1,SNORA14A,ST8SIA3,TH,TTC36

FNDC9,CDH19,DPP6,ELAVL3,GAP43,GNG3,NEFM, NGB,NOS1,PHOX2A,PHOX2B,PLP1,PRIMA1,PRPH, SLC18A3,SLC5A7,SORCS1,SOX10,ST8SIA3,STMN4,SYT9	ASTN1,ATCAY,ATP1A3,CELF4,CNTN2,CTNNA2,DNER, DPYSL5,INA,KIF1A,KIF5A,L1CAM,MYT1L,NEFL, NEFM,PHOX2B,RET,SLC7A14,ST8SIA3,SYT1,TMEM130

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

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for ST8SIA3

There's no related Drug.

Top

Cross referenced IDs for ST8SIA3

* 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