Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 HAS3
Basic gene info.Gene symbolHAS3
Gene namehyaluronan synthase 3
Synonyms-
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :69141442-69151570
Type of geneprotein-coding
RefGenesNM_001199280.1,
NM_005329.2,NM_138612.2,
Ensembl idENSG00000103044
DescriptionHA synthase 3hyaluronate synthase 3hyaluronic acid synthase 3
Modification date20141207
dbXrefs MIM : 602428
HGNC : HGNC
Ensembl : ENSG00000103044
HPRD : 03889
Vega : OTTHUMG00000137562
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HAS3
BioGPS: 3038
Gene Expression Atlas: ENSG00000103044
The Human Protein Atlas: ENSG00000103044
PathwayNCI Pathway Interaction Database: HAS3
KEGG: HAS3
REACTOME: HAS3
ConsensusPathDB
Pathway Commons: HAS3
MetabolismMetaCyc: HAS3
HUMANCyc: HAS3
RegulationEnsembl's Regulation: ENSG00000103044
miRBase: chr16 :69,141,442-69,151,570
TargetScan: NM_001199280
cisRED: ENSG00000103044
ContextiHOP: HAS3
cancer metabolism search in PubMed: HAS3
UCL Cancer Institute: HAS3
Assigned class in ccmGDBC

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Phenotypic Information for HAS3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HAS3
Familial Cancer Database: HAS3
* 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_HYALURONAN_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HAS3
MedGen: HAS3 (Human Medical Genetics with Condition)
ClinVar: HAS3
PhenotypeMGI: HAS3 (International Mouse Phenotyping Consortium)
PhenomicDB: HAS3

Mutations for HAS3
* 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
ovaryHAS3chr166914602269146042VPS4Achr166935359469353614
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 HAS3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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
There's no copy number variation information in COSMIC data for this gene.

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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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=27)
Stat. for Synonymous SNVs
(# total SNVs=10)
Stat. for Deletions
(# total SNVs=1)
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
chr16:69143446-69143446p.A50T3
chr16:69148815-69148815p.M436I2
chr16:69148611-69148611p.N368K2
chr16:69143815-69143815p.R173C1
chr16:69143412-69143412p.T38T1
chr16:69148326-69148326p.C273C1
chr16:69148719-69148719p.G404G1
chr16:69143634-69143634p.S112S1
chr16:69143820-69143820p.V174V1
chr16:69148385-69148385p.S293T1

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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
# sample31171 3121 421  5519
# mutation41171 3121 421  55112
nonsynonymous SNV2115  3111 221  3419
synonymous SNV2  21   1  2    21 3
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
chr16:69148496p.R330Q,HAS33
chr16:69148385p.S293T,HAS32
chr16:69148799p.H276R1
chr16:69143627p.T38T,HAS31
chr16:69143862p.E160K,HAS31
chr16:69143365p.A50T,HAS31
chr16:69148326p.R173C,HAS31
chr16:69148916p.L56Q,HAS31
chr16:69143684p.V174V,HAS31
chr16:69143877p.T334T,HAS31

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 HAS3 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 HAS3

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

BNC1,C11orf87,CDH4,COL17A1,FGFBP1,HAS3,HMGA2,
HSD17B3,KRT5,KRT75,LOC150527,MIR31HG,MT4,MYO7B,
OR2J3,PADI3,PCSK9,PLEK2,RPSAP52,S100A2,SOX15
AEN,CD200,CDK2,CLDN1,DYRK3,HAS3,HEY2,
HSPA4L,IFFO2,KRT23,KRT9,LAMC2,LIF,NPAS4,
PLK3,SRF,STK17A,TES,TUFT1,WEE1,ZNF165

CRCT1,CRNN,DEFB103B,HAS3,IL36A,KLK9,KRT14,
KRT16,KRT6A,KRT6C,KRT78,LCE3D,LCE3E,LYPD3,
SPRR1B,SPRR2A,SPRR2B,SPRR2C,SPRR2D,SPRR2E,TGM1
ADRA2A,B4GALT1,FABP1,HAS3,HSD17B2,KRT12,LANCL3,
LOC25845,MIER3,OSTalpha,PLOD2,PPARD,PPP1R14C,SLC20A1,
SLC30A10,SLC4A9,SLC9A3,TGFA,TMEM65,WSCD1,ZNF341
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 HAS3


There's no related Drug.
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Cross referenced IDs for HAS3
* 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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