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 symbolST3GAL1
Gene nameST3 beta-galactoside alpha-2,3-sialyltransferase 1
SynonymsGal-NAc6S|SIAT4A|SIATFL|ST3GalA|ST3GalA.1|ST3GalIA|ST3GalIA,1|ST3O
CytomapUCSC genome browser: 8q24.22
Genomic locationchr8 :134467090-134584183
Type of geneprotein-coding
RefGenesNM_003033.3,
NM_173344.2,
Ensembl idENSG00000008513
DescriptionCMP-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 date20141207
dbXrefs MIM : 607187
HGNC : HGNC
Ensembl : ENSG00000008513
HPRD : 06219
Vega : OTTHUMG00000164534
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ST3GAL1
BioGPS: 6482
Gene Expression Atlas: ENSG00000008513
The Human Protein Atlas: ENSG00000008513
PathwayNCI Pathway Interaction Database: ST3GAL1
KEGG: ST3GAL1
REACTOME: ST3GAL1
ConsensusPathDB
Pathway Commons: ST3GAL1
MetabolismMetaCyc: ST3GAL1
HUMANCyc: ST3GAL1
RegulationEnsembl's Regulation: ENSG00000008513
miRBase: chr8 :134,467,090-134,584,183
TargetScan: NM_003033
cisRED: ENSG00000008513
ContextiHOP: ST3GAL1
cancer metabolism search in PubMed: ST3GAL1
UCL Cancer Institute: ST3GAL1
Assigned class in ccmGDBC

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Phenotypic Information for ST3GAL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ST3GAL1
MedGen: ST3GAL1 (Human Medical Genetics with Condition)
ClinVar: ST3GAL1
PhenotypeMGI: ST3GAL1 (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
haematopoietic_and_lymphoid_tissueST3GAL1chr8134529352134529352ST3GAL1chr8134529352134529352
liverST3GAL1chr8134485385134485385UVRAGchr117560176975601769
ovaryST3GAL1chr8134548364134548384ST3GAL1chr8134548616134548636
ovaryST3GAL1chr8134555011134555031ST3GAL1chr8134555076134555096
pancreasST3GAL1chr8134529100134529120ST3GAL1chr8134529269134529289
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows ST3GAL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF329641NPNT103444106880206106888601ST3GAL13425088134502882134503048
BG005080AES14811930541363054215ST3GAL1781378134475787134475847
BI005060NEMF2250145025194850256016ST3GAL12405448134468265134468570
BI015032HNRNPL44138193933321639333309ST3GAL11293218134468546134468738
CB250683ST3GAL1191398134467093134467213ST3GAL11362538134467266134467383

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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample5 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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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=3

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check002.gifSomatic 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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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
chr8:134474202-134474202p.V255V3
chr8:134474124-134474124p.C281C3
chr8:134488007-134488007p.T87T3
chr8:134472081-134472081p.D317N2
chr8:134472091-134472091p.T313T2
chr8:134472163-134472163p.F289F2
chr8:134478159-134478159p.D161H2
chr8:134488260-134488260p.T3N2
chr8:134472027-134472027p.R335W2
chr8:134488080-134488080p.H63R2

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22 71   2  65  176 7
# mutation22 71   2  65  177 6
nonsynonymous SNV11 31   1  34   55 2
synonymous SNV11 4    1  31  122 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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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
chr8:134474202p.V255V,ST3GAL13
chr8:134472027p.R335W,ST3GAL12
chr8:134472060p.H316Q,ST3GAL11
chr8:134488056p.T211T,ST3GAL11
chr8:134478196p.R68C,ST3GAL11
chr8:134472082p.K312N,ST3GAL11
chr8:134488066p.G199E,ST3GAL11
chr8:134475669p.I54M,ST3GAL11
chr8:134478210p.A291T,ST3GAL11
chr8:134472094p.K184K,ST3GAL11

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 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

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

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
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 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



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