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 ST3GAL1

Basic gene info.	Gene symbol	ST3GAL1
	Gene name	ST3 beta-galactoside alpha-2,3-sialyltransferase 1
	Synonyms	Gal-NAc6S\|SIAT4A\|SIATFL\|ST3GalA\|ST3GalA.1\|ST3GalIA\|ST3GalIA,1\|ST3O
	Cytomap	UCSC genome browser: 8q24.22
	Genomic location	chr8 :134467090-134584183
	Type of gene	protein-coding
	RefGenes	NM_003033.3, NM_173344.2,
	Ensembl id	ENSG00000008513
	Description	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase 1Gal-beta-1,3-GalNAc-alpha-2,3-sialyltransferaseSIAT4-AST3GalIalpha 2,3-ST 1beta-galactoside alpha-2,3-sialyltransferase 1sialyltransferase 4A (beta-galactosidase alpha-2,3-sialy
	Modification date	20141207
dbXrefs	MIM : 607187
	HGNC : HGNC
	Ensembl : ENSG00000008513
	HPRD : 06219
	Vega : OTTHUMG00000164534
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ST3GAL1
	BioGPS: 6482
	Gene Expression Atlas: ENSG00000008513
	The Human Protein Atlas: ENSG00000008513
Pathway	NCI Pathway Interaction Database: ST3GAL1
	KEGG: ST3GAL1
	REACTOME: ST3GAL1
	ConsensusPathDB
	Pathway Commons: ST3GAL1
Metabolism	MetaCyc: ST3GAL1
	HUMANCyc: ST3GAL1
Regulation	Ensembl's Regulation: ENSG00000008513
	miRBase: chr8 :134,467,090-134,584,183
	TargetScan: NM_003033
	cisRED: ENSG00000008513
Context	iHOP: ST3GAL1
	cancer metabolism search in PubMed: ST3GAL1
	UCL Cancer Institute: ST3GAL1
Assigned class in ccmGDB	C

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Phenotypic Information for ST3GAL1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ST3GAL1
	Familial Cancer Database: ST3GAL1

* 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 REACTOME_METABOLISM_OF_CARBOHYDRATES

Others
OMIM
Orphanet
Disease	KEGG Disease: ST3GAL1
	MedGen: ST3GAL1 (Human Medical Genetics with Condition)
	ClinVar: ST3GAL1
Phenotype	MGI: ST3GAL1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ST3GAL1

Mutations for ST3GAL1

* 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

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- For Inter-chromosomal Variations

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
haematopoietic_and_lymphoid_tissue	ST3GAL1	chr8	134529352	134529352	ST3GAL1	chr8	134529352	134529352
liver	ST3GAL1	chr8	134485385	134485385	UVRAG	chr11	75601769	75601769
ovary	ST3GAL1	chr8	134548364	134548384	ST3GAL1	chr8	134548616	134548636
ovary	ST3GAL1	chr8	134555011	134555031	ST3GAL1	chr8	134555076	134555096
pancreas	ST3GAL1	chr8	134529100	134529120	ST3GAL1	chr8	134529269	134529289

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 ST3GAL1 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
BF329641	NPNT	10	344	4	106880206	106888601	ST3GAL1	342	508	8	134502882	134503048
BG005080	AES	14	81	19	3054136	3054215	ST3GAL1	78	137	8	134475787	134475847
BI005060	NEMF	2	250	14	50251948	50256016	ST3GAL1	240	544	8	134468265	134468570
BI015032	HNRNPL	44	138	19	39333216	39333309	ST3GAL1	129	321	8	134468546	134468738
CB250683	ST3GAL1	19	139	8	134467093	134467213	ST3GAL1	136	253	8	134467266	134467383

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

Mutation type/ Tissue ID	brca	cns	cerv	endome	haematopo	kidn	Lintest	liver	lung	ns	ovary	pancre	prost	skin	stoma	thyro	urina
Total # sample	5		1				1		2		1		1		1		1
GAIN (# sample)	5		1				1		2		1		1		1		1
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)

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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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=25)	Stat. for Synonymous SNVs (# total SNVs=21)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr8:134474202-134474202	p.V255V	3
chr8:134474124-134474124	p.C281C	3
chr8:134488007-134488007	p.T87T	3
chr8:134472081-134472081	p.D317N	2
chr8:134472091-134472091	p.T313T	2
chr8:134472163-134472163	p.F289F	2
chr8:134478159-134478159	p.D161H	2
chr8:134488260-134488260	p.T3N	2
chr8:134472027-134472027	p.R335W	2
chr8:134488080-134488080	p.H63R	2

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

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
chr8:134474202	p.V255V,ST3GAL1	3
chr8:134472027	p.R335W,ST3GAL1	2
chr8:134472060	p.H316Q,ST3GAL1	1
chr8:134488056	p.T211T,ST3GAL1	1
chr8:134478196	p.R68C,ST3GAL1	1
chr8:134472082	p.K312N,ST3GAL1	1
chr8:134488066	p.G199E,ST3GAL1	1
chr8:134475669	p.I54M,ST3GAL1	1
chr8:134478210	p.A291T,ST3GAL1	1
chr8:134472094	p.K184K,ST3GAL1	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 ST3GAL1 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 ST3GAL1

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


ARFGEF1,ATP6V1C1,C8orf33,DERL1,FAM84B,FAM91A1,IMPAD1, KIAA0196,KIAA1429,PTK2,ST3GAL1,STAU2,TMED10P1,UBE2W, UBR5,UTP23,VPS13B,WWP1,ZNF252P,ZNF623,ZNF7	ABCA1,ANO6,CPM,CS,RMDN1,FZD4,GBE1, GPT2,HSDL2,ITGA7,KIAA0408,LIMS1,PCYT1A,PFKFB1, PLIN5,PTPRM,RAB2A,RNF157,ST3GAL1,STBD1,YWHAG

ACADL,ASAP1,MILR1,C20orf194,CCDC88A,CHST15,ELK3, FAM20A,GLRB,ITPRIP,PPP1R18,MCC,MDFIC,MSN, NKX6-1,PABPC4L,QKI,RAI14,SPATA8,ST3GAL1,ST8SIA2	ADCY7,ATM,CARD8,CLSTN3,DENND4B,FCHSD2,FLI1, KCNAB2,MYO5A,NLRP1,ODF2,PAPLN,PLXND1,PREX1, RHBDF2,SEC14L1,SH2D3C,ST3GAL1,TBC1D2B,WDFY2,ZNF469

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 ST3GAL1

There's no related Drug.

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Cross referenced IDs for ST3GAL1

* 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