Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 HSPG2
Basic gene info.Gene symbolHSPG2
Gene nameheparan sulfate proteoglycan 2
SynonymsHSPG|PLC|PRCAN|SJA|SJS|SJS1
CytomapUCSC genome browser: 1p36.1-p34
Genomic locationchr1 :22148736-22263750
Type of geneprotein-coding
RefGenesNM_001291860.1,
NM_005529.6,
Ensembl idENSG00000142798
Descriptionbasement membrane-specific heparan sulfate proteoglycan core proteinendorepellin (domain V region)perlecan proteoglycan
Modification date20141207
dbXrefs MIM : 142461
HGNC : HGNC
Ensembl : ENSG00000142798
HPRD : 00804
Vega : OTTHUMG00000002674
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSPG2
BioGPS: 3339
Gene Expression Atlas: ENSG00000142798
The Human Protein Atlas: ENSG00000142798
PathwayNCI Pathway Interaction Database: HSPG2
KEGG: HSPG2
REACTOME: HSPG2
ConsensusPathDB
Pathway Commons: HSPG2
MetabolismMetaCyc: HSPG2
HUMANCyc: HSPG2
RegulationEnsembl's Regulation: ENSG00000142798
miRBase: chr1 :22,148,736-22,263,750
TargetScan: NM_001291860
cisRED: ENSG00000142798
ContextiHOP: HSPG2
cancer metabolism search in PubMed: HSPG2
UCL Cancer Institute: HSPG2
Assigned class in ccmGDBC

Top
Phenotypic Information for HSPG2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSPG2
Familial Cancer Database: HSPG2
* 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_LIPIDS_AND_LIPOPROTEINS
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_LIPOPROTEIN_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: HSPG2
MedGen: HSPG2 (Human Medical Genetics with Condition)
ClinVar: HSPG2
PhenotypeMGI: HSPG2 (International Mouse Phenotyping Consortium)
PhenomicDB: HSPG2

Mutations for HSPG2
* 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
There's no intra-chromosomal structural variation.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSPG2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CD676182HSPG2120812221278922212997MOV102046251113242372113243187
AW604468HSPG22534012224195922242274HSPG233765012220671122207023
AW855179EIF3B32348724054572405778HSPG233641612217857522178654
BE927253HSPG22033912220670522207023HSPG233664612224196422242274

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample 1               
GAIN (# sample) 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)

Top
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=11

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=244)
Stat. for Synonymous SNVs
(# total SNVs=105)
Stat. for Deletions
(# total SNVs=5)
Stat. for Insertions
(# total SNVs=1)

Top
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
chr1:22149935-22149935p.S4350S11
chr1:22191454-22191454p.A1503V7
chr1:22176683-22176683p.L2433V4
chr1:22165987-22165987p.H3256Y3
chr1:22174253-22174253p.V2652M3
chr1:22214000-22214000p.A291T3
chr1:22182404-22182404p.A1859A3
chr1:22214554-22214554p.Q194*3
chr1:22150680-22150680p.G4278V3
chr1:22222458-22222458p.D67D3

Top
check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample983237 1321022281612 53529 25
# mutation1383247 1421022321612 54436 38
nonsynonymous SNV761157 9291125119 42523 25
synonymous SNV6229  5 111753 11913 13
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])

Top
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
chr1:22206927p.R2698L,HSPG22
chr1:22183650p.F912F,HSPG22
chr1:22173921p.P1534P,HSPG22
chr1:22203098p.I3831I,HSPG22
chr1:22191363p.S709S,HSPG22
chr1:22214000p.N1812N,HSPG22
chr1:22174253p.V2653M,HSPG22
chr1:22154901p.R4087W,HSPG22
chr1:22168062p.I2635I,HSPG22
chr1:22174305p.V1659M,HSPG22

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 HSPG2 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]

Top
Gene Expression for HSPG2

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

BCL6B,VSTM4,CD93,CDH5,COL15A1,GPR124,HEG1,
HSPG2,KIAA1462,LAMA4,LRP1,LRRC32,NOTCH4,PDGFRB,
PHLDB1,PODN,RHOJ,STARD8,SYNPO,TIE1,TNS1
SYNE3,FAM212B,CDC42BPB,COL4A1,COL4A2,DAAM2,DOCK6,
EHD2,HSPG2,ITGA7,KANK2,CTIF,LRP1,MCAM,
MPRIP,MYO1C,PLIN4,PTPRS,PXDN,TFE3,TLN1

ARHGEF17,CD93,COL4A2,COL8A1,DDR2,EHD2,EMILIN1,
ENG,FBN1,FLT4,GPR124,HEG1,HSPG2,IL1R1,
LAMA4,LAMC1,MMRN2,PXDN,STARD8,TIE1,VWF
AHDC1,AHNAK2,AR,CNTNAP1,COL15A1,COL4A1,COL4A2,
DCHS1,FLNA,GLI2,HSPG2,IGSF9B,LDLRAD2,MAP1A,
MICALL1,NACC2,NID1,PXDN,SETBP1,TLN1,VCL
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for HSPG2


There's no related Drug.
Top
Cross referenced IDs for HSPG2
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas