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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for CHST3 |
Basic gene info. | Gene symbol | CHST3 |
Gene name | carbohydrate (chondroitin 6) sulfotransferase 3 | |
Synonyms | C6ST|C6ST1|HSD | |
Cytomap | UCSC genome browser: 10q22.1 | |
Genomic location | chr10 :73724119-73773322 | |
Type of gene | protein-coding | |
RefGenes | NM_004273.4, | |
Ensembl id | ENSG00000122863 | |
Description | C6ST-1GST-0carbohydrate sulfotransferase 3chondroitin 6-O-sulfotransferase 1galactose/N-acetylglucosamine/N-acetylglucosamine 6-O-sulfotransferase 0 | |
Modification date | 20141219 | |
dbXrefs | MIM : 603799 | |
HGNC : HGNC | ||
Ensembl : ENSG00000122863 | ||
HPRD : 07052 | ||
Vega : OTTHUMG00000018431 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_CHST3 | |
BioGPS: 9469 | ||
Gene Expression Atlas: ENSG00000122863 | ||
The Human Protein Atlas: ENSG00000122863 | ||
Pathway | NCI Pathway Interaction Database: CHST3 | |
KEGG: CHST3 | ||
REACTOME: CHST3 | ||
ConsensusPathDB | ||
Pathway Commons: CHST3 | ||
Metabolism | MetaCyc: CHST3 | |
HUMANCyc: CHST3 | ||
Regulation | Ensembl's Regulation: ENSG00000122863 | |
miRBase: chr10 :73,724,119-73,773,322 | ||
TargetScan: NM_004273 | ||
cisRED: ENSG00000122863 | ||
Context | iHOP: CHST3 | |
cancer metabolism search in PubMed: CHST3 | ||
UCL Cancer Institute: CHST3 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for CHST3(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: CHST3 |
Familial Cancer Database: CHST3 |
* 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: CHST3 |
MedGen: CHST3 (Human Medical Genetics with Condition) | |
ClinVar: CHST3 | |
Phenotype | MGI: CHST3 (International Mouse Phenotyping Consortium) |
PhenomicDB: CHST3 |
Mutations for CHST3 |
* 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 |
- 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 |
There's no intra-chromosomal structural variation. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
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 CHST3 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 |
Other DBs for Structural Variants |
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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 |   |   | |||
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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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=33) | (# total SNVs=14) |
(# total SNVs=2) | (# total SNVs=1) |
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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 |
chr10:73767738-73767738 | p.K317* | 2 |
chr10:73767316-73767316 | p.P176L | 2 |
chr10:73767922-73767922 | p.P378L | 2 |
chr10:73765714-73765714 | p.I38I | 2 |
chr10:73767705-73767705 | p.V306M | 2 |
chr10:73767393-73767393 | p.V202M | 1 |
chr10:73765727-73765727 | p.I44fs*9 | 1 |
chr10:73767717-73767717 | p.R310C | 1 |
chr10:73767281-73767281 | p.P164P | 1 |
chr10:73768143-73768143 | p.G452S | 1 |
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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 |   | 1 | 1 | 7 |   |   |   | 2 |   | 1 |   | 4 | 2 |   |   |   |   | 5 |   | 4 |
# mutation |   | 1 | 1 | 8 |   |   |   | 2 |   | 1 |   | 4 | 2 |   |   |   |   | 5 |   | 5 |
nonsynonymous SNV |   |   | 1 | 6 |   |   |   |   |   | 1 |   | 2 | 1 |   |   |   |   | 3 |   | 4 |
synonymous SNV |   | 1 |   | 2 |   |   |   | 2 |   |   |   | 2 | 1 |   |   |   |   | 2 |   | 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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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 |
chr10:73767297 | p.R170C | 2 |
chr10:73765714 | p.I38M | 2 |
chr10:73768179 | p.A127A | 1 |
chr10:73767039 | p.D458D | 1 |
chr10:73767393 | p.R142H | 1 |
chr10:73767080 | p.A460T | 1 |
chr10:73767691 | p.F162F | 1 |
chr10:73767095 | p.N464D | 1 |
chr10:73767717 | p.A181A | 1 |
chr10:73767170 | p.G183C | 1 |
Other DBs for Point Mutations |
Copy Number for CHST3 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 CHST3 |
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 |
ACTN1,BOC,C22orf23,CCDC82,CHST3,GLS,HAPLN3, MAML2,MFGE8,MICALL1,MRAS,MSN,MYLK,PRNP, PTPN14,RGMA,SOX6,SUN2,TIAM2,TRPV4,WWTR1 | ACTN1,ACTN4,ADAMTS15,ANKS1A,BCR,CHST3,DZIP1L, ERRFI1,FAT1,FLNA,FOXO3,FOXO3B,KLF7,LTBP2, MYH9,NCKAP5L,OSR1,PER1,SPTAN1,USP4,WDR81 | ||||
ARHGEF17,CLMP,CHST3,COL8A1,DDR2,DSEL,EFS, EHD2,EMILIN1,EVC,FBN1,FBXL7,GLI3,GPR124, HEG1,KIAA1462,MRC2,NRP2,PKD2,PTRF,TSHZ3 | ARHGEF17,BOC,CHST3,COL4A1,COL6A1,COL6A2,DCHS1, EFS,FBXL7,FGFR1,FSTL1,HSPA12A,LAMA4,LAMC1, NLGN2,NPR2,PTPRM,RUSC2,SDK1,SLC12A4,SLC16A2 |
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 CHST3 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB01248 | carbohydrate (chondroitin 6) sulfotransferase 3 | approved; investigational | Docetaxel | ||
DB01041 | carbohydrate (chondroitin 6) sulfotransferase 3 | approved; withdrawn; investigational | Thalidomide |
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Cross referenced IDs for CHST3 |
* 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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