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| Phenotypic Information (metabolism pathway, cancer, disease, phenome) |
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| Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG |
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| Gene Summary for ST6GALNAC3 |
| Basic gene info. | Gene symbol | ST6GALNAC3 |
| Gene name | ST6 (alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3)-N-acetylgalactosaminide alpha-2,6-sialyltransferase 3 | |
| Synonyms | PRO7177|SIAT7C|ST6GALNACIII|STY | |
| Cytomap | UCSC genome browser: 1p31.1 | |
| Genomic location | chr1 :76540388-77042892 | |
| Type of gene | protein-coding | |
| RefGenes | NM_001160011.1, NM_152996.2, | |
| Ensembl id | ENSG00000184005 | |
| Description | GalNAc 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 date | 20141207 | |
| dbXrefs | MIM : 610133 | |
| HGNC : HGNC | ||
| Ensembl : ENSG00000184005 | ||
| HPRD : 15341 | ||
| Vega : OTTHUMG00000009615 | ||
| Protein | UniProt: Q8NDV1 go to UniProt's Cross Reference DB Table | |
| Expression | CleanEX: HS_ST6GALNAC3 | |
| BioGPS: 256435 | ||
| Gene Expression Atlas: ENSG00000184005 | ||
| The Human Protein Atlas: ENSG00000184005 | ||
| Pathway | NCI Pathway Interaction Database: ST6GALNAC3 | |
| KEGG: ST6GALNAC3 | ||
| REACTOME: ST6GALNAC3 | ||
| ConsensusPathDB | ||
| Pathway Commons: ST6GALNAC3 | ||
| Metabolism | MetaCyc: ST6GALNAC3 | |
| HUMANCyc: ST6GALNAC3 | ||
| Regulation | Ensembl's Regulation: ENSG00000184005 | |
| miRBase: chr1 :76,540,388-77,042,892 | ||
| TargetScan: NM_001160011 | ||
| cisRED: ENSG00000184005 | ||
| Context | iHOP: ST6GALNAC3 | |
| cancer metabolism search in PubMed: ST6GALNAC3 | ||
| UCL Cancer Institute: ST6GALNAC3 | ||
| Assigned class in ccmGDB | B - This gene belongs to cancer gene. | |
| Top |
| Phenotypic Information for ST6GALNAC3(metabolism pathway, cancer, disease, phenome) |
 Cancer Description | |
| Cancer | CGAP: ST6GALNAC3 |
| Familial Cancer Database: ST6GALNAC3 | |
| * This gene is included in those cancer gene databases. |
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Oncogene 1 | Significant driver gene in | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
| 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 | |
| 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. |
| Structural Variants in COSMIC: go to COSMIC mutation histogram |
| - Statistics for Tissue and Mutation type | Top |
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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'. |
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| - 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'. |
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| Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
| breast | ST6GALNAC3 | chr1 | 76724131 | 76724131 | ST6GALNAC3 | chr1 | 76724209 | 76724209 |
| breast | ST6GALNAC3 | chr1 | 77010021 | 77010021 | chr14 | 84659003 | 84659003 | |
| ovary | ST6GALNAC3 | chr1 | 76707692 | 76707712 | ST6GALNAC3 | chr1 | 76658960 | 76658980 |
| ovary | ST6GALNAC3 | chr1 | 77040224 | 77040244 | ST6GALNAC3 | chr1 | 77040343 | 77040363 |
| pancreas | ST6GALNAC3 | chr1 | 76545329 | 76545349 | ST6GALNAC3 | chr1 | 76564076 | 76564096 |
| pancreas | ST6GALNAC3 | chr1 | 76547672 | 76547692 | CCDC18 | chr1 | 93737627 | 93737647 |
| pancreas | ST6GALNAC3 | chr1 | 76647721 | 76647741 | chr1 | 76482932 | 76482952 | |
| pancreas | ST6GALNAC3 | chr1 | 76651029 | 76651049 | ST6GALNAC3 | chr1 | 76651081 | 76651101 |
| pancreas | ST6GALNAC3 | chr1 | 76758833 | 76758853 | ST6GALNAC3 | chr1 | 76768961 | 76768981 |
| pancreas | ST6GALNAC3 | chr1 | 76903971 | 76903991 | chr17 | 46569445 | 46569465 | |
| skin | ST6GALNAC3 | chr1 | 76832222 | 76832222 | chr1 | 103213639 | 103213639 | |
| skin | ST6GALNAC3 | chr1 | 77027911 | 77027911 | chr1 | 105803874 | 105803874 |
| 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 ST6GALNAC3 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 |
| BF093713 | ST6GALNAC3 | 131 | 150 | 1 | 76907439 | 76907458 | SEC14L1 | 144 | 399 | 17 | 75202737 | 75202992 | |
| BG003526 | ADAM12 | 3 | 255 | 10 | 127886468 | 127886721 | ST6GALNAC3 | 250 | 272 | 1 | 76769836 | 76769864 | |
| Other DBs for Structural Variants |
| Top |
| 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 | 1 | 1 | 4 | 3 | 1 | 1 | 2 | 1 | ||||||||||||
| GAIN (# sample) | 1 | 2 | 1 | 1 | 2 | 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) |
| Top |
| SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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: Non-synonymous mutation, 
: Synonymous mutation, Circle size denotes number of samples. |
| Top |
| Somatic Mutation Counts per Tissue in COSMIC data |
| Stat. for Non-Synonymous SNVs (# total SNVs=72) | (# total SNVs=13) |
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(# total SNVs=0) | (# total SNVs=1) |
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| Top |
| 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 |
| chr1:76779647-76779647 | p.R59Q | 5 |
| chr1:76877876-76877876 | p.V133I | 4 |
| chr1:76877830-76877830 | p.E117E | 3 |
| chr1:77093180-77093180 | p.L223I | 3 |
| chr1:76877767-76877767 | p.N96K | 2 |
| chr1:76877855-76877855 | p.R126* | 2 |
| chr1:77094406-77094406 | p.R278K | 2 |
| chr1:76877778-76877778 | p.R100Q | 2 |
| chr1:76779491-76779491 | p.R7I | 2 |
| chr1:76779609-76779609 | p.K46N | 2 |
| Top |
| SNV Counts per Each Loci in TCGA data |
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| 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 | 1 | 14 | 2 | 6 | 1 | 10 | 4 | 3 | 5 | 6 | 7 | ||||||||
| # mutation | 2 | 1 | 12 | 2 | 6 | 1 | 10 | 4 | 3 | 5 | 6 | 9 | ||||||||
| nonsynonymous SNV | 2 | 1 | 8 | 1 | 5 | 1 | 9 | 4 | 2 | 4 | 6 | 8 | ||||||||
| synonymous SNV | 5 | 1 | 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]) |
| Top |
| 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 |
| chr1:76877830 | p.E117E,ST6GALNAC3 | 3 |
| chr1:76779491 | p.R59Q,ST6GALNAC3 | 2 |
| chr1:76779492 | p.R7I,ST6GALNAC3 | 2 |
| chr1:77094406 | p.R7R,ST6GALNAC3 | 2 |
| chr1:76779647 | p.R278K | 2 |
| chr1:76878011 | p.V133I,ST6GALNAC3 | 1 |
| chr1:76779542 | p.V199D,ST6GALNAC3 | 1 |
| chr1:77093237 | p.R55S,ST6GALNAC3 | 1 |
| chr1:76877711 | p.P134P,ST6GALNAC3 | 1 |
| chr1:76877888 | p.A225T | 1 |
| Other DBs for Point Mutations |
| Copy 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. |
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| 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] |
| Top |
| Gene Expression for ST6GALNAC3 |
| 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. |
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| 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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| Top |
| 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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| Top |
| 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
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| 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 |
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| 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 |
| Co-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
| Top |
| Interacting Genes (from Pathway Commons) |
: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID
| Top |
| Pharmacological Information for ST6GALNAC3 |
| There's no related Drug. |
| Top |
| 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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