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 ST8SIA6
Basic gene info.Gene symbolST8SIA6
Gene nameST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6
SynonymsSIA8F|SIAT8F|ST8SIA-VI
CytomapUCSC genome browser: 10p12.33
Genomic locationchr10 :17362675-17496254
Type of geneprotein-coding
RefGenesNM_001004470.1,
Ensembl idENSG00000148488
DescriptionSIAT8-FST8SiaVIalpha-2,8-sialyltransferase 8Falpha-2,8-sialyltransferase 8F variant 2alpha-2,8-sialyltransferase 8F variant 3sialyltransferase 8F (alpha-2, 8-sialyltransferase)sialyltransferase St8Sia VIsialytransferase St8Sia VI
Modification date20141207
dbXrefs MIM : 610139
HGNC : HGNC
HPRD : 15344
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ST8SIA6
BioGPS: 338596
Gene Expression Atlas: ENSG00000148488
The Human Protein Atlas: ENSG00000148488
PathwayNCI Pathway Interaction Database: ST8SIA6
KEGG: ST8SIA6
REACTOME: ST8SIA6
ConsensusPathDB
Pathway Commons: ST8SIA6
MetabolismMetaCyc: ST8SIA6
HUMANCyc: ST8SIA6
RegulationEnsembl's Regulation: ENSG00000148488
miRBase: chr10 :17,362,675-17,496,254
TargetScan: NM_001004470
cisRED: ENSG00000148488
ContextiHOP: ST8SIA6
cancer metabolism search in PubMed: ST8SIA6
UCL Cancer Institute: ST8SIA6
Assigned class in ccmGDBC

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Phenotypic Information for ST8SIA6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: ST8SIA6
Familial Cancer Database: ST8SIA6
* 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: ST8SIA6
MedGen: ST8SIA6 (Human Medical Genetics with Condition)
ClinVar: ST8SIA6
PhenotypeMGI: ST8SIA6 (International Mouse Phenotyping Consortium)
PhenomicDB: ST8SIA6

Mutations for ST8SIA6
* 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
pancreasST8SIA6chr101740650817406528NEBLchr102120558821205608
pancreasST8SIA6chr101742101617421036chr102728239427282414
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 ST8SIA6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA780464TNFSF912081965358686536075ST8SIA6198440101743209317432338
AI954707ST8SIA61213101739023717390449ST8SIA6207546101738398817384327

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 # sample          1     1
GAIN (# sample)          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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=60)
Stat. for Synonymous SNVs
(# total SNVs=25)
Stat. for Deletions
(# total SNVs=5)
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
chr10:17363274-17363274p.L267P4
chr10:17363321-17363321p.A252fs*534
chr10:17369027-17369027p.S207S4
chr10:17362951-17362951p.E375*3
chr10:17363217-17363217p.T286M2
chr10:17432535-17432535p.T95T2
chr10:17363170-17363170p.K302*2
chr10:17401513-17401513p.R126K2
chr10:17363049-17363049p.G342V2
chr10:17363200-17363200p.A292S2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 111   32 1681  37 7
# mutation12 101   32 1681  37 7
nonsynonymous SNV12 81   21 1051  26 3
synonymous SNV   2    11 63   11 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
chr10:17363274p.L267P4
chr10:17369027p.S207S2
chr10:17363213p.L287L2
chr10:17432598p.S74S2
chr10:17363049p.G342V1
chr10:17373510p.I240R1
chr10:17432586p.V140A1
chr10:17369028p.A50A1
chr10:17363050p.G342R1
chr10:17373535p.S223I1

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 ST8SIA6 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 ST8SIA6

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

AFF1,ANKRD30A,ASH1L,CCDC176,KIAA0825,CACNA1D,DIXDC1,
DNAJC16,DTWD2,HNRNPH2,INADL,CIPC,KIF13B,MAP3K1,
RALGPS2,SETBP1,SPATA6,ST8SIA6,ZBTB41,ZNF43,ZNF619
ANKRD30A,ENPP5,ERBB4,INPP4B,IQCH,LRBA,MPP7,
MYB,MYO6,NR6A1,JADE3,PRLR,RABEP1,RALGPS1,
RALGPS2,RASEF,RFX6,ST8SIA6,TBC1D9,WNK3,ZNF396

ACSL3,ALDH18A1,ARHGAP18,ATE1,DCTN5,ELOVL5,FOXN2,
GLDC,IPMK,LIN7A,MAPK14,MPP7,NOMO2,PAPD5,
PLOD2,RAB30,SCD,SLC11A2,ST8SIA6,TDP2,VPS35
ALDOA,ARF3,BTBD3,CEACAM7,FAM120AOS,FUT3,GRAMD3,
HIST1H2BD,IFNGR2,LCMT1,LITAF,LRP4,MFSD5,NETO2,
OPN3,PEX26,PGM1,PLOD2,SLC16A3,ST8SIA6,TMEM171
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 ST8SIA6


There's no related Drug.
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Cross referenced IDs for ST8SIA6
* 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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