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 HPSE2
Basic gene info.Gene symbolHPSE2
Gene nameheparanase 2 (inactive)
SynonymsHPA2|HPR2|UFS|UFS1
CytomapUCSC genome browser: 10q23-q24
Genomic locationchr10 :100216833-100995632
Type of geneprotein-coding
RefGenesNM_001166244.1,
NM_001166245.1,NM_001166246.1,NM_021828.4,
Ensembl idENSG00000172987
Descriptionheparanase 3heparanase-like proteininactive heparanase-2
Modification date20141219
dbXrefs MIM : 613469
HGNC : HGNC
HPRD : 13669
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HPSE2
BioGPS: 60495
Gene Expression Atlas: ENSG00000172987
The Human Protein Atlas: ENSG00000172987
PathwayNCI Pathway Interaction Database: HPSE2
KEGG: HPSE2
REACTOME: HPSE2
ConsensusPathDB
Pathway Commons: HPSE2
MetabolismMetaCyc: HPSE2
HUMANCyc: HPSE2
RegulationEnsembl's Regulation: ENSG00000172987
miRBase: chr10 :100,216,833-100,995,632
TargetScan: NM_001166244
cisRED: ENSG00000172987
ContextiHOP: HPSE2
cancer metabolism search in PubMed: HPSE2
UCL Cancer Institute: HPSE2
Assigned class in ccmGDBC

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Phenotypic Information for HPSE2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HPSE2
Familial Cancer Database: HPSE2
* 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_METABOLISM_OF_CARBOHYDRATES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HPSE2
MedGen: HPSE2 (Human Medical Genetics with Condition)
ClinVar: HPSE2
PhenotypeMGI: HPSE2 (International Mouse Phenotyping Consortium)
PhenomicDB: HPSE2

Mutations for HPSE2
* 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
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- 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
breastHPSE2chr10100508078100508078HPSE2chr10100519761100519761
ovaryHPSE2chr10100243402100243422HPSE2chr10100275889100275909
ovaryHPSE2chr10100494884100494904HPSE2chr10100494977100494997
ovaryHPSE2chr10100556624100556644HPSE2chr10100539287100539307
pancreasHPSE2chr10100489665100489685chr109792797097927990
pancreasHPSE2chr10100718513100718533chr182824660528246625
pancreasHPSE2chr10100872248100872448chr183967584839676048
pancreasHPSE2chr10100973456100973476HPSE2chr10100980342100980362
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 HPSE2 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample33  1   1 3   12 
GAIN (# sample)3                
LOSS (# sample) 3  1   1 3   12 
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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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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=83)
Stat. for Synonymous SNVs
(# total SNVs=28)
Stat. for Deletions
(# total SNVs=2)
Stat. for Insertions
(# total SNVs=2)

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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
chr10:100995386-100995386p.K58N4
chr10:100481571-100481571p.R267W4
chr10:100503793-100503793p.Y211H3
chr10:100219419-100219419p.R564Q3
chr10:100219428-100219428p.R561H3
chr10:100249954-100249954p.?2
chr10:100503679-100503679p.A249T2
chr10:100503680-100503680p.S248S2
chr10:100374721-100374721p.R420R2
chr10:100374727-100374727p.V418V2

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample121193 4 3  1342  35 12
# mutation121193 5 4  1442  45 16
nonsynonymous SNV   152 2 3  922  13 10
synonymous SNV12151 3 1  52   32 7
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
chr10:100995386p.K58K,HPSE25
chr10:100374727p.V344V,HPSE22
chr10:100219419p.R155W,HPSE22
chr10:100249906p.R452Q,HPSE22
chr10:100219428p.S248S,HPSE22
chr10:100481571p.R449H,HPSE22
chr10:100995356p.V306V,HPSE22
chr10:100503680p.K68K,HPSE22
chr10:100401655p.G351G,HPSE21
chr10:100904127p.Q248L,HPSE21

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 HPSE2 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 HPSE2

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

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
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 HPSE2


There's no related Drug.
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Cross referenced IDs for HPSE2
* 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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