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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for HPSE |
Basic gene info. | Gene symbol | HPSE |
Gene name | heparanase | |
Synonyms | HPA|HPA1|HPR1|HPSE1|HSE1 | |
Cytomap | UCSC genome browser: 4q21.3 | |
Genomic location | chr4 :84213613-84256034 | |
Type of gene | protein-coding | |
RefGenes | NM_001098540.2, NM_001166498.2,NM_001199830.1,NM_006665.5, | |
Ensembl id | ENSG00000173083 | |
Description | endo-glucoronidaseheparanase-1 | |
Modification date | 20141207 | |
dbXrefs | MIM : 604724 | |
HGNC : HGNC | ||
Ensembl : ENSG00000173083 | ||
HPRD : 05286 | ||
Vega : OTTHUMG00000130425 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_HPSE | |
BioGPS: 10855 | ||
Gene Expression Atlas: ENSG00000173083 | ||
The Human Protein Atlas: ENSG00000173083 | ||
Pathway | NCI Pathway Interaction Database: HPSE | |
KEGG: HPSE | ||
REACTOME: HPSE | ||
ConsensusPathDB | ||
Pathway Commons: HPSE | ||
Metabolism | MetaCyc: HPSE | |
HUMANCyc: HPSE | ||
Regulation | Ensembl's Regulation: ENSG00000173083 | |
miRBase: chr4 :84,213,613-84,256,034 | ||
TargetScan: NM_001098540 | ||
cisRED: ENSG00000173083 | ||
Context | iHOP: HPSE | |
cancer metabolism search in PubMed: HPSE | ||
UCL Cancer Institute: HPSE | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for HPSE(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: HPSE |
Familial Cancer Database: HPSE |
* 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_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: HPSE |
MedGen: HPSE (Human Medical Genetics with Condition) | |
ClinVar: HPSE | |
Phenotype | MGI: HPSE (International Mouse Phenotyping Consortium) |
PhenomicDB: HPSE |
Mutations for HPSE |
* 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 |
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'. |
Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | HPSE | chr4 | 84244483 | 84244503 | chr4 | 129502467 | 129502487 |
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 HPSE 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 |
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=48) | (# total SNVs=15) |
(# total SNVs=1) | (# 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 |
chr4:84227368-84227368 | p.F398F | 5 |
chr4:84222192-84222192 | p.R465W | 3 |
chr4:84231914-84231914 | p.V268A | 3 |
chr4:84223361-84223361 | p.V423M | 2 |
chr4:84231203-84231203 | p.D291H | 2 |
chr4:84243475-84243475 | p.A90A | 2 |
chr4:84230558-84230558 | p.F327L | 2 |
chr4:84231915-84231915 | p.V268I | 2 |
chr4:84230599-84230599 | p.D314N | 2 |
chr4:84234371-84234371 | p.A190V | 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 | 2 | 3 |   | 12 | 3 |   | 2 |   | 1 | 1 |   | 4 | 4 | 1 |   | 1 | 9 | 7 |   | 8 |
# mutation | 3 | 3 |   | 11 | 3 |   | 2 |   | 1 | 1 |   | 4 | 4 | 1 |   | 1 | 9 | 6 |   | 10 |
nonsynonymous SNV | 3 | 3 |   | 9 | 3 |   | 2 |   | 1 |   |   | 2 | 3 | 1 |   | 1 | 5 | 6 |   | 6 |
synonymous SNV |   |   |   | 2 |   |   |   |   |   | 1 |   | 2 | 1 |   |   |   | 4 |   |   | 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 |
chr4:84227368 | p.F340F,HPSE | 4 |
chr4:84222192 | p.V210A,HPSE | 3 |
chr4:84231914 | p.R391W,HPSE | 3 |
chr4:84231203 | p.A190V,HPSE | 2 |
chr4:84234371 | p.D233H,HPSE | 2 |
chr4:84231915 | p.V210I,HPSE | 2 |
chr4:84231969 | p.E273G,HPSE | 1 |
chr4:84222179 | p.S182S,HPSE | 1 |
chr4:84227440 | p.K388T,HPSE | 1 |
chr4:84243394 | p.S264F,HPSE | 1 |
Other DBs for Point Mutations |
Copy Number for HPSE 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 HPSE |
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 |
ADCYAP1R1,AKR7A2P1,ANKK1,ASZ1,EBF2,FIGF,FLJ46111, GRIN1,HAO2,HPSE2,KIRREL3,KRT3,MYH11,OR51A2, PTPN5,TAGLN3,TGM4,TNNI3K,TPH2,TWISTNB,ZCCHC12 | ALX4,C1orf95,FRRS1L,CAPN6,CNTN1,CRMP1,DLK1, FHAD1,FMO1,HPSE2,INSRR,KCNMB2,LAMC3,LPAR4, MMP16,NEO1,PRDM8,RELN,SERINC5,SLC26A5,TMEM130 |
ATP2B3,CACNG7,CHRNA4,CHST8,DPYSL5,GPR26,GPR50, HPSE2,NMRK2,LOC200726,NCAN,P2RX2,PCSK2,PNPLA5, RP1-177G6.2,RPRM,SELV,SHISA7,SLC1A6,SYCP1,TFAP2B | ALDH5A1,ALDH6A1,ATMIN,CNTN4,EPB41,HPSE2,KIAA1109, MSI1,PTPRT,R3HDM2,RAD50,STOX2,SYNJ2,TBC1D4, TBC1D5,TNKS,VGLL4,ZBTB44,ZNF318,ZNF395,ZNF808 |
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 HPSE |
There's no related Drug. |
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Cross referenced IDs for HPSE |
* 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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