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 HSPB1
Basic gene info.Gene symbolHSPB1
Gene nameheat shock 27kDa protein 1
SynonymsCMT2F|HEL-S-102|HMN2B|HS.76067|HSP27|HSP28|Hsp25|SRP27
CytomapUCSC genome browser: 7q11.23
Genomic locationchr7 :75931874-75933614
Type of geneprotein-coding
RefGenesNM_001540.3,
Ensembl idENSG00000106211
Description28 kDa heat shock proteinHSP 27epididymis secretory protein Li 102estrogen-regulated 24 kDa proteinheat shock 27 kDa proteinheat shock 27kD protein 1heat shock protein beta-1stress-responsive protein 27
Modification date20141219
dbXrefs MIM : 602195
HGNC : HGNC
Ensembl : ENSG00000106211
HPRD : 09076
Vega : OTTHUMG00000023228
ProteinUniProt: P04792
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HSPB1
BioGPS: 3315
Gene Expression Atlas: ENSG00000106211
The Human Protein Atlas: ENSG00000106211
PathwayNCI Pathway Interaction Database: HSPB1
KEGG: HSPB1
REACTOME: HSPB1
ConsensusPathDB
Pathway Commons: HSPB1
MetabolismMetaCyc: HSPB1
HUMANCyc: HSPB1
RegulationEnsembl's Regulation: ENSG00000106211
miRBase: chr7 :75,931,874-75,933,614
TargetScan: NM_001540
cisRED: ENSG00000106211
ContextiHOP: HSPB1
cancer metabolism search in PubMed: HSPB1
UCL Cancer Institute: HSPB1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HSPB1 in cancer cell metabolism1. Sun X, Ou Z, Xie M, Kang R, Fan Y, et al. (2015) HSPB1 as a novel regulator of ferroptotic cancer cell death. Oncogene. doi: 10.1038/onc.2015.32. go to article

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Phenotypic Information for HSPB1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HSPB1
Familial Cancer Database: HSPB1
* 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_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 602195; gene.
602195; gene.
606595; phenotype.
606595; phenotype.
608634; phenotype.
608634; phenotype.
Orphanet 139525; Distal hereditary motor neuropathy type 2.
139525; Distal hereditary motor neuropathy type 2.
99940; Autosomal dominant Charcot-Marie-Tooth disease type 2F.
99940; Autosomal dominant Charcot-Marie-Tooth disease type 2F.
DiseaseKEGG Disease: HSPB1
MedGen: HSPB1 (Human Medical Genetics with Condition)
ClinVar: HSPB1
PhenotypeMGI: HSPB1 (International Mouse Phenotyping Consortium)
PhenomicDB: HSPB1

Mutations for HSPB1
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HSPB1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA903814HSPB118577593353375933895EGR1772125137801706137802528
AJ710478SKP122575133496716133509692HSPB125736577593201675932124
BU737515HSPB1199477593353775933612STXBP1894139130454104130454428
DA893722TNNC21173204445322444455951HSPB117247577593224275933388
CD387519HSPB12422877593199075932194UBE2M226934195906736759069801
DA283619HSPB1111377593199275932104RAPGEF511257572215950022159963
N36356RMRP225293565775335658003HSPB124952977593223675933353
AI470274HSPB186577593354875933605FARP2582022242382597242382741
R77849GJC11224174287877442878996HSPB122029877593353575933612
Z23090XPO546048464350660143506625HSPB1478123177593201675933612
AI609727HSPB1141777593206675933611HSPB141245977593332875933375
BU631277HSPB1259477593353575933603WASF1875866110423249110426758
DA537518HSPB119977593199475932092OBSL1845402220432891220435250
AI123558HSPB146977593354475933609DDX1757418223888418938884549
AI801539HSPB12416977593345775933602HSPB116548877593207175932394
CA336509HSPB127877593299275933068KRT1974186173967986939679981

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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=6)
Stat. for Synonymous SNVs
(# total SNVs=2)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.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
chr7:75932058-75932058p.L10H1
chr7:75932122-75932122p.Q31Q1
chr7:75932270-75932270p.L81I1
chr7:75932376-75932376p.G116V1
chr7:75933134-75933134p.R127Q1
chr7:75933348-75933348p.P159H1
chr7:75933373-75933373p.A167A1
chr7:75933408-75933408p.I179N1
chr7:75933416-75933416p.P182S1
chr7:75933446-75933446p.G192W1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   2       121  21  
# mutation   2       121  21  
nonsynonymous SNV   1       1 1  2   
synonymous SNV   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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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
chr7:75932122p.L81I1
chr7:75932270p.A167A1
chr7:75933373p.P170P1
chr7:75933382p.I179N1
chr7:75933408p.P182S1
chr7:75933416p.G192W1
chr7:75933446p.A204A1
chr7:75933484p.L10H1
chr7:75932058p.Q31Q1

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 HSPB1 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 HSPB1

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

BLOC1S1,BOLA2,C12orf10,IFT43,C16orf13,TSR3,ECI1,
MZT2B,FAM173A,FAM195A,HSPB1,JOSD2,MRPL28,MRPS34,
NDUFA2,NDUFB10,NOSIP,NUBP2,TCEB2,PAM16,ZNHIT1
ARAF,COX17,COX8A,DEXI,ENDOG,HCFC1R1,HSPB1,
LSM10,LINC00116,NDUFB10,NDUFB2,NDUFS7,NDUFS8,PGP,
PHPT1,SEPW1,SLC16A3,SLC25A11,EMC6,UBAC1,UQCR10

C7orf61,CDKN2A,DHDH,FLJ25758,IZUMO1R,GAGE12D,GAGE4,
HIST1H2BI,HSPB1,LOC728392,LRRC7,MS4A13,OXT,PFN3,
RHBDD2,SEPW1,SSX2,TMEM88,TUBG2,VAT1,ZFAND2A
ACTG2,CCDC136,CNN1,CTNNA3,CTXN1,DES,DMPK,
DNAJB5,FAM46B,FLNA,FLNC,HSPB1,HSPB7,ILDR2,
KY,LDB3,PDLIM7,PYGM,SLC2A4,SMTN,TAGLN
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 HSPB1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P04792; -.
ChemistryChEMBL CHEMBL5976; -.
ChemistryBindingDB P04792; -.
ChemistryChEMBL CHEMBL5976; -.
Organism-specific databasesPharmGKB PA29511; -.
Organism-specific databasesPharmGKB PA29511; -.
Organism-specific databasesCTD 3315; -.
Organism-specific databasesCTD 3315; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00125heat shock 27kDa protein 1approved; nutraceuticalL-Arginine
DB00435heat shock 27kDa protein 1approvedNitric Oxide
DB00269heat shock 27kDa protein 1approvedChlorotrianisene
DB00286heat shock 27kDa protein 1approvedConjugated Estrogens
DB00890heat shock 27kDa protein 1approvedDienestrol
DB00255heat shock 27kDa protein 1approvedDiethylstilbestrol
DB00783heat shock 27kDa protein 1approved; investigationalEstradiol
DB00655heat shock 27kDa protein 1approvedEstrone
DB00977heat shock 27kDa protein 1approvedEthinyl Estradiol
DB00143heat shock 27kDa protein 1approved; nutraceuticalGlutathione


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Cross referenced IDs for HSPB1
* 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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