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 ST6GAL1
Basic gene info.Gene symbolST6GAL1
Gene nameST6 beta-galactosamide alpha-2,6-sialyltranferase 1
SynonymsSIAT1|ST6GalI|ST6N
CytomapUCSC genome browser: 3q27-q28
Genomic locationchr3 :186648314-186796341
Type of geneprotein-coding
RefGenesNM_003032.2,
NM_173216.2,NM_173217.2,
Ensembl idENSG00000073849
DescriptionB-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 date20141207
dbXrefs MIM : 109675
HGNC : HGNC
Ensembl : ENSG00000073849
HPRD : 00184
Vega : OTTHUMG00000156500
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ST6GAL1
BioGPS: 6480
Gene Expression Atlas: ENSG00000073849
The Human Protein Atlas: ENSG00000073849
PathwayNCI Pathway Interaction Database: ST6GAL1
KEGG: ST6GAL1
REACTOME: ST6GAL1
ConsensusPathDB
Pathway Commons: ST6GAL1
MetabolismMetaCyc: ST6GAL1
HUMANCyc: ST6GAL1
RegulationEnsembl's Regulation: ENSG00000073849
miRBase: chr3 :186,648,314-186,796,341
TargetScan: NM_003032
cisRED: ENSG00000073849
ContextiHOP: ST6GAL1
cancer metabolism search in PubMed: ST6GAL1
UCL Cancer Institute: ST6GAL1
Assigned class in ccmGDBC

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Phenotypic Information for ST6GAL1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ST6GAL1
MedGen: ST6GAL1 (Human Medical Genetics with Condition)
ClinVar: ST6GAL1
PhenotypeMGI: ST6GAL1 (International Mouse Phenotyping Consortium)
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.

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

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryST6GAL1chr3186661562186661582KNG1chr3186459634186459654
ovaryST6GAL1chr3186683386186683406HRGchr3186388940186388960
ovaryST6GAL1chr3186778691186778711ATP13A3chr3194141829194141849
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 ST6GAL1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM919650LPP-AS219883187871740187871809ST6GAL1829783186790631186793956
AW609212UBE2R2442193391766633918089ST6GAL14145993186794510186794695
DR002138ST6GAL193903186794864186795245ST6GAL13907233186681643186760571
AI032739GRN2114174243035842430470ST6GAL11085833186760877186792004
AA705426GRN2114174243035842430470ST6GAL11084913186760969186792004
AA973233MRPS3412701618218931822162ST6GAL12633513186795577186795665

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 # sample12      3 3 1    
GAIN (# sample)12      3 2 1    
LOSS (# sample)          1      
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=2

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check002.gifSomatic 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.

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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
chr3:186760790-186760790p.S100I2
chr3:186761061-186761061p.A190A2
chr3:186760565-186760565p.V25E2
chr3:186761082-186761082p.Q197H2
chr3:186760883-186760883p.P131L2
chr3:186760670-186760670p.S60F1
chr3:186791973-186791973p.F277L1
chr3:186760924-186760924p.R145W1
chr3:186760515-186760515p.K8N1
chr3:186769117-186769117p.R230C1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample2  51 2 1  321  71 5
# mutation2  41 2 1  321  71 7
nonsynonymous SNV1  21      22   4  6
synonymous SNV1  3  2 1  1 1  31 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])

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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
chr3:186791973p.A190A,ST6GAL12
chr3:186761061p.F277F,ST6GAL12
chr3:186760790p.S100I,ST6GAL12
chr3:186760840p.L18I,ST6GAL11
chr3:186791960p.P170P,ST6GAL11
chr3:186760543p.V22V,ST6GAL11
chr3:186760866p.E28K,ST6GAL11
chr3:186760557p.G191R,ST6GAL11
chr3:186760883p.L51L,ST6GAL11
chr3:186792044p.R230C,ST6GAL11

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 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]

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Gene Expression for ST6GAL1

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

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
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 ST6GAL1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00301ST6 beta-galactosamide alpha-2,6-sialyltranferase 1approvedFlucloxacillin


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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



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