Cancer Cell Metabolism Gene Database

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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 ST6GALNAC3
Basic gene info.Gene symbolST6GALNAC3
Gene nameST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3
SynonymsPRO7177|SIAT7C|ST6GALNACIII|STY
CytomapUCSC genome browser: 1p31.1
Genomic locationchr1 :76540388-77042892
Type of geneprotein-coding
RefGenesNM_001160011.1,
NM_152996.2,
Ensembl idENSG00000184005
DescriptionGalNAc alpha-2,6-sialyltransferase IIISIAT7-CST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltranST6GALNAC IIIalpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3alpha-N-acetylgalactosaminide alp
Modification date20141207
dbXrefs MIM : 610133
HGNC : HGNC
Ensembl : ENSG00000184005
HPRD : 15341
Vega : OTTHUMG00000009615
ProteinUniProt: Q8NDV1
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ST6GALNAC3
BioGPS: 256435
Gene Expression Atlas: ENSG00000184005
The Human Protein Atlas: ENSG00000184005
PathwayNCI Pathway Interaction Database: ST6GALNAC3
KEGG: ST6GALNAC3
REACTOME: ST6GALNAC3
ConsensusPathDB
Pathway Commons: ST6GALNAC3
MetabolismMetaCyc: ST6GALNAC3
HUMANCyc: ST6GALNAC3
RegulationEnsembl's Regulation: ENSG00000184005
miRBase: chr1 :76,540,388-77,042,892
TargetScan: NM_001160011
cisRED: ENSG00000184005
ContextiHOP: ST6GALNAC3
cancer metabolism search in PubMed: ST6GALNAC3
UCL Cancer Institute: ST6GALNAC3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for ST6GALNAC3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ST6GALNAC3
Familial Cancer Database: ST6GALNAC3
* 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 610133; gene.
Orphanet
DiseaseKEGG Disease: ST6GALNAC3
MedGen: ST6GALNAC3 (Human Medical Genetics with Condition)
ClinVar: ST6GALNAC3
PhenotypeMGI: ST6GALNAC3 (International Mouse Phenotyping Consortium)
PhenomicDB: ST6GALNAC3

Mutations for ST6GALNAC3
* 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
breastST6GALNAC3chr17672413176724131ST6GALNAC3chr17672420976724209
breastST6GALNAC3chr17701002177010021chr148465900384659003
ovaryST6GALNAC3chr17670769276707712ST6GALNAC3chr17665896076658980
ovaryST6GALNAC3chr17704022477040244ST6GALNAC3chr17704034377040363
pancreasST6GALNAC3chr17654532976545349ST6GALNAC3chr17656407676564096
pancreasST6GALNAC3chr17654767276547692CCDC18chr19373762793737647
pancreasST6GALNAC3chr17664772176647741chr17648293276482952
pancreasST6GALNAC3chr17665102976651049ST6GALNAC3chr17665108176651101
pancreasST6GALNAC3chr17675883376758853ST6GALNAC3chr17676896176768981
pancreasST6GALNAC3chr17690397176903991chr174656944546569465
skinST6GALNAC3chr17683222276832222chr1103213639103213639
skinST6GALNAC3chr17702791177027911chr1105803874105803874
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 ST6GALNAC3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF093713ST6GALNAC313115017690743976907458SEC14L1144399177520273775202992
BG003526ADAM12325510127886468127886721ST6GALNAC325027217676983676769864

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 # sample1  1  4 3 1  12 1
GAIN (# sample)1       2 1  12 1
LOSS (# sample)   1  4 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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=72)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr1:76779647-76779647p.R59Q5
chr1:76877876-76877876p.V133I4
chr1:76877830-76877830p.E117E3
chr1:77093180-77093180p.L223I3
chr1:76779497-76779497p.S9Y2
chr1:76877903-76877903p.Y142H2
chr1:76877919-76877919p.A147V2
chr1:76877752-76877752p.G91G2
chr1:76877767-76877767p.N96K2
chr1:76877855-76877855p.R126*2

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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
# sample21 142 6 1  1043  56 7
# mutation21 122 6 1  1043  56 9
nonsynonymous SNV21 81 5 1  942  46 8
synonymous SNV   51 1    1 1  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])

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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
chr1:76877830p.E117E,ST6GALNAC33
chr1:77094406p.R278K2
chr1:76779647p.R59Q,ST6GALNAC32
chr1:76779491p.R7I,ST6GALNAC32
chr1:76779492p.R7R,ST6GALNAC32
chr1:76877834p.L173L,ST6GALNAC31
chr1:76779494p.H277N1
chr1:76877955p.A18V,ST6GALNAC31
chr1:76779638p.G178C,ST6GALNAC31
chr1:77093212p.V24A,ST6GALNAC31

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 ST6GALNAC3 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 ST6GALNAC3

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

BMX,CHRDL1,ELTD1,EMCN,ERG,FAT4,GPR116,
LDB2,MCTP1,MEOX1,MEOX2,MYCT1,PPAP2B,PREX2,
PTPRB,RHOJ,SPRY1,ST6GALNAC3,TEK,TGFBR2,ZNF366
ABLIM3,ARHGAP31,BTNL9,CCDC85A,CD36,EPAS1,F8,
FLT1,GPR116,KIAA1462,MYCT1,PDE8A,PTPRM,ST6GALNAC3,
SV2B,TACC1,TEK,TMC7,SLC35G2,UVRAG,VAMP3

ADAM22,CXCR4,DYNC2H1,GNG2,HACE1,HOMER2,KIR3DL3,
LIX1L,LOC145845,NEK1,OSBPL8,PIK3CG,PRAMEF1,PRKAR2B,
SH2D1B,SHISA2,SMR3A,SMR3B,SP4,ST6GALNAC3,TTYH1
AMPH,AP3M2,PLET1,C7orf61,CBX1,CN5H6.4,CUL4B,
FAM124B,HIGD1B,KBTBD6,LOC220930,MGC57346,NAP1L1,PEX12,
RFTN2,SAV1,ST6GALNAC3,TMEM169,ZNF569,ZNF610,ZNF788
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 ST6GALNAC3


There's no related Drug.
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Cross referenced IDs for ST6GALNAC3
* 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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