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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CHST6 |
Basic gene info. | Gene symbol | CHST6 |
Gene name | carbohydrate (N-acetylglucosamine 6-O) sulfotransferase 6 | |
Synonyms | MCDC1 | |
Cytomap | UCSC genome browser: 16q22 | |
Genomic location | chr16 :75507021-75528926 | |
Type of gene | protein-coding | |
RefGenes | NM_021615.4, | |
Ensembl id | ENSG00000183196 | |
Description | C-GlcNAc6STGST4-betaN-acetylglucosamine 6-O-sulfotransferase 5carbohydrate sulfotransferase 6corneal N-acetylglucosamine 6-sulfotransferasecorneal N-acetylglucosamine-6-O-sulfotransferasegalactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotra | |
Modification date | 20141207 | |
dbXrefs | MIM : 605294 | |
HGNC : HGNC | ||
Ensembl : ENSG00000183196 | ||
HPRD : 05597 | ||
Vega : OTTHUMG00000137612 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CHST6 | |
BioGPS: 4166 | ||
Gene Expression Atlas: ENSG00000183196 | ||
The Human Protein Atlas: ENSG00000183196 | ||
Pathway | NCI Pathway Interaction Database: CHST6 | |
KEGG: CHST6 | ||
REACTOME: CHST6 | ||
ConsensusPathDB | ||
Pathway Commons: CHST6 | ||
Metabolism | MetaCyc: CHST6 | |
HUMANCyc: CHST6 | ||
Regulation | Ensembl's Regulation: ENSG00000183196 | |
miRBase: chr16 :75,507,021-75,528,926 | ||
TargetScan: NM_021615 | ||
cisRED: ENSG00000183196 | ||
Context | iHOP: CHST6 | |
cancer metabolism search in PubMed: CHST6 | ||
UCL Cancer Institute: CHST6 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CHST6(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CHST6 |
Familial Cancer Database: CHST6 |
* This gene is included in those cancer gene databases. |
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_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: CHST6 |
MedGen: CHST6 (Human Medical Genetics with Condition) | |
ClinVar: CHST6 | |
Phenotype | MGI: CHST6 (International Mouse Phenotyping Consortium) |
PhenomicDB: CHST6 |
Mutations for CHST6 |
* 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 |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows CHST6 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 |
AF219990 | CHST6 | 1 | 2069 | 16 | 75512350 | 75529282 | COTL1 | 2070 | 2521 | 16 | 84599202 | 84599653 |
Other DBs for Structural Variants |
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Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=56) | (# total SNVs=13) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr16:75513386-75513386 | p.R114H | 3 |
chr16:75513561-75513561 | p.V56M | 3 |
chr16:75512546-75512546 | p.R394Q | 3 |
chr16:75512762-75512762 | p.S322L | 3 |
chr16:75513562-75513562 | p.F55F | 2 |
chr16:75512725-75512725 | p.R334R | 2 |
chr16:75513568-75513568 | p.S53S | 2 |
chr16:75512862-75512862 | p.A289T | 2 |
chr16:75512732-75512732 | p.A332V | 2 |
chr16:75513330-75513330 | p.P133T | 2 |
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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 | 3 |   | 1 | 8 | 2 |   | 12 |   |   |   | 1 | 7 | 5 | 1 | 1 |   | 7 | 10 |   | 7 |
# mutation | 3 |   | 1 | 7 | 2 |   | 12 |   |   |   | 1 | 7 | 5 | 1 | 1 |   | 7 | 11 |   | 10 |
nonsynonymous SNV | 1 |   | 1 | 5 | 2 |   | 6 |   |   |   | 1 | 5 | 5 | 1 | 1 |   | 4 | 9 |   | 6 |
synonymous SNV | 2 |   |   | 2 |   |   | 6 |   |   |   |   | 2 |   |   |   |   | 3 | 2 |   | 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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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 |
chr16:75512725 | p.R334R | 3 |
chr16:75512895 | p.F55F | 2 |
chr16:75512732 | p.A289T | 2 |
chr16:75513508 | p.R278W | 2 |
chr16:75512907 | p.A73A | 2 |
chr16:75512862 | p.E274K | 2 |
chr16:75513562 | p.A332V | 2 |
chr16:75513474 | p.H249L | 1 |
chr16:75513666 | p.P139L | 1 |
chr16:75513075 | p.R316H | 1 |
Other DBs for Point Mutations |
Copy Number for CHST6 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 CHST6 |
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. |
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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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
BAG2,C17orf51,CALU,CHST3,CHST6,DLX6,DLX6AS, FAT1,FOXL1,GLG1,GLS,MAML2,MDFI,MET, MICALL1,PLOD1,PTK7,RAB23,SFT2D2,SOX6,UCA1 | ADAM8,ATP6V0D2,BEAN,CD300LF,CHST11,CHST6,CNGB1, DGKA,GAL3ST4,HTRA4,IKBKE,LILRA4,PITPNM1,PKD2L1, SDS,SH3BP1,SLC38A5,TMEM51,TNC,UBASH3B,UNC13D |
B3GNT9,C11orf24,TMEM263,CHST6,CREB3L1,FAM114A1,FUT8, GAS2L1,GJB5,GPX8,HIF1A,IKBIP,KCNK6,KDELR3, PDE4D,RELL1,SEC24D,SEMA4B,SIX4,SLC16A2,TANC2 | ABHD12,C10orf54,C1orf115,CCL14-CCL15,CDHR5,CHST6,EPS8L2, FAM102A,INPP5J,KIAA1211,KIAA2013,LOC151534,MEP1A,NGEF, PC,PDLIM2,PLA2G12B,RIN2,RIPK4,TMEM120A,TMEM150B |
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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for CHST6 |
There's no related Drug. |
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Cross referenced IDs for CHST6 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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