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 ST6GAL1

Basic gene info.	Gene symbol	ST6GAL1
	Gene name	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1
	Synonyms	SIAT1\|ST6GalI\|ST6N
	Cytomap	UCSC genome browser: 3q27-q28
	Genomic location	chr3 :186648314-186796341
	Type of gene	protein-coding
	RefGenes	NM_003032.2, NM_173216.2,NM_173217.2,
	Ensembl id	ENSG00000073849
	Description	B-cell antigen CD75CMP-N-acetylneuraminate beta-galactosamide alpha-2,6-sialyltransferaseCMP-N-acetylneuraminate-beta-galactosamide-alpha-2,6-sialyltransferase 1ST6Gal Ialpha 2,6-ST 1beta-galactoside alpha-2,6-sialyltransferase 1sialyltransferase 1
	Modification date	20141207
dbXrefs	MIM : 109675
	HGNC : HGNC
	Ensembl : ENSG00000073849
	HPRD : 00184
	Vega : OTTHUMG00000156500
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ST6GAL1
	BioGPS: 6480
	Gene Expression Atlas: ENSG00000073849
	The Human Protein Atlas: ENSG00000073849
Pathway	NCI Pathway Interaction Database: ST6GAL1
	KEGG: ST6GAL1
	REACTOME: ST6GAL1
	ConsensusPathDB
	Pathway Commons: ST6GAL1
Metabolism	MetaCyc: ST6GAL1
	HUMANCyc: ST6GAL1
Regulation	Ensembl's Regulation: ENSG00000073849
	miRBase: chr3 :186,648,314-186,796,341
	TargetScan: NM_003032
	cisRED: ENSG00000073849
Context	iHOP: ST6GAL1
	cancer metabolism search in PubMed: ST6GAL1
	UCL Cancer Institute: ST6GAL1
Assigned class in ccmGDB	C

Top

Phenotypic Information for ST6GAL1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ST6GAL1
	Familial Cancer Database: ST6GAL1

* 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: ST6GAL1
	MedGen: ST6GAL1 (Human Medical Genetics with Condition)
	ClinVar: ST6GAL1
Phenotype	MGI: ST6GAL1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ST6GAL1

Mutations for ST6GAL1

* 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

- Statistics for Tissue and Mutation type

Top

- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	ST6GAL1	chr3	186661562	186661582	KNG1	chr3	186459634	186459654
ovary	ST6GAL1	chr3	186683386	186683406	HRG	chr3	186388940	186388960
ovary	ST6GAL1	chr3	186778691	186778711	ATP13A3	chr3	194141829	194141849

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ST6GAL1 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
BM919650	LPP-AS2	19	88	3	187871740	187871809	ST6GAL1	82	978	3	186790631	186793956
AW609212	UBE2R2	4	421	9	33917666	33918089	ST6GAL1	414	599	3	186794510	186794695
DR002138	ST6GAL1	9	390	3	186794864	186795245	ST6GAL1	390	723	3	186681643	186760571
AI032739	GRN	2	114	17	42430358	42430470	ST6GAL1	108	583	3	186760877	186792004
AA705426	GRN	2	114	17	42430358	42430470	ST6GAL1	108	491	3	186760969	186792004
AA973233	MRPS34	1	270	16	1821893	1822162	ST6GAL1	263	351	3	186795577	186795665

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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=2

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=28)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr3:186760790-186760790	p.S100I	2
chr3:186761061-186761061	p.A190A	2
chr3:186760565-186760565	p.V25E	2
chr3:186761082-186761082	p.Q197H	2
chr3:186760883-186760883	p.P131L	2
chr3:186760557-186760557	p.V22V	1
chr3:186790707-186790707	p.P259Q	1
chr3:186793465-186793465	p.T365T	1
chr3:186790722-186790722	p.S264*	1
chr3:186760840-186760840	p.L117L	1

Top

SNV Counts per Each Loci in TCGA data

: non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

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	2			5	1		2		1			3	2	1			7	1		5
# mutation	2			4	1		2		1			3	2	1			7	1		7
nonsynonymous SNV	1			2	1							2	2				4			6
synonymous SNV	1			3			2		1			1		1			3	1		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])

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
chr3:186761061	p.F277F,ST6GAL1	2
chr3:186760790	p.S100I,ST6GAL1	2
chr3:186791973	p.A190A,ST6GAL1	2
chr3:186760650	p.S60F,ST6GAL1	1
chr3:186760952	p.P273L,ST6GAL1	1
chr3:186793484	p.T68T,ST6GAL1	1
chr3:186760670	p.R75C,ST6GAL1	1
chr3:186761001	p.P301L,ST6GAL1	1
chr3:186793540	p.G79V,ST6GAL1	1
chr3:186760695	p.S346C,ST6GAL1	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 ST6GAL1 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 ST6GAL1

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


ACSL1,ACSL5,ACTR3,APOL6,ASS1,CFLAR,CP, FNDC3B,GK3P,GLYATL2,LIMCH1,MTUS1,RASSF5,RNF217, SEL1L3,SLC15A2,SLC25A18,SLC5A1,SLFN11,ST6GAL1,TMEM123	ABCC2,ABCC4,AFMID,ALOX15B,C6orf223,CHST1,CLNK, EAF2,ELOVL7,FABP7,HPGD,KYNU,LST-3TM12,PNLIPRP3, PPAPDC1A,SGPP2,ST6GAL1,STARD4,TARP,TLR7,TMPRSS11F

ABAT,AOAH,ATP9A,KIAA0226L,GDPD5,GPR160,KLHL24, LRRC2,PLAGL2,PLCB4,POFUT1,PRLR,SATB2,SERINC3, ST6GAL1,STAU1,TGIF2,TM9SF4,TMEM192,ZBTB38,ZSWIM3	ATP2C2,TMEM254,C9orf152,CPA6,FLJ23867,KIAA1147,KIAA1324, LOC284578,MARCKSL1,MTL5,NEURL1,NRAP,PTPRO,RXFP4, SAMD10,SEC14L5,SLC2A10,ST6GAL1,ST6GALNAC1,STAG3,WNK4

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 ST6GAL1

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
DB00301	ST6 beta-galactosamide alpha-2,6-sialyltranferase 1	approved	Flucloxacillin

Top

Cross referenced IDs for ST6GAL1

* 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