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 HMOX1
Basic gene info.Gene symbolHMOX1
Gene nameheme oxygenase (decycling) 1
SynonymsHMOX1D|HO-1|HSP32|bK286B10
CytomapUCSC genome browser: 22q13.1
Genomic locationchr22 :35777059-35790207
Type of geneprotein-coding
RefGenesNM_002133.2,
Ensembl idENSG00000100292
Descriptionheat shock protein, 32-kDheme oxygenase 1
Modification date20141222
dbXrefs MIM : 141250
HGNC : HGNC
Ensembl : ENSG00000100292
HPRD : 00782
Vega : OTTHUMG00000150960
ProteinUniProt: P09601
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_HMOX1
BioGPS: 3162
Gene Expression Atlas: ENSG00000100292
The Human Protein Atlas: ENSG00000100292
PathwayNCI Pathway Interaction Database: HMOX1
KEGG: HMOX1
REACTOME: HMOX1
ConsensusPathDB
Pathway Commons: HMOX1
MetabolismMetaCyc: HMOX1
HUMANCyc: HMOX1
RegulationEnsembl's Regulation: ENSG00000100292
miRBase: chr22 :35,777,059-35,790,207
TargetScan: NM_002133
cisRED: ENSG00000100292
ContextiHOP: HMOX1
cancer metabolism search in PubMed: HMOX1
UCL Cancer Institute: HMOX1
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HMOX1 in cancer cell metabolism1. Biswas C, Shah N, Muthu M, La P, Fernando AP, et al. (2014) Nuclear heme oxygenase-1 (HO-1) modulates subcellular distribution and activation of Nrf2, impacting metabolic and anti-oxidant defenses. J Biol Chem 289: 26882-26894. doi: 10.1074/jbc.M114.567685. pmid: 4175329. go to article
2. Schmidt A, Dietrich S, Steuer A, Weltmann KD, von Woedtke T, et al. (2015) Non-thermal plasma activates human keratinocytes by stimulation of antioxidant and phase II pathways. J Biol Chem 290: 6731-6750. doi: 10.1074/jbc.M114.603555. pmid: 4358097. go to article
3. Lee PJ, Shin I, Seo SY, Kim H, Kim HP (2014) Upregulation of both heme oxygenase-1 and ATPase inhibitory factor 1 renders tumoricidal activity by synthetic flavonoids via depleting cellular ATP. Bioorg Med Chem Lett 24: 4845-4849. doi: 10.1016/j.bmcl.2014.08.055 go to article

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Phenotypic Information for HMOX1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: HMOX1
Familial Cancer Database: HMOX1
* 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
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM
REACTOME_METABOLISM_OF_PORPHYRINS

check002.gifOthers
OMIM 141250; gene.
614034; phenotype.
Orphanet
DiseaseKEGG Disease: HMOX1
MedGen: HMOX1 (Human Medical Genetics with Condition)
ClinVar: HMOX1
PhenotypeMGI: HMOX1 (International Mouse Phenotyping Consortium)
PhenomicDB: HMOX1

Mutations for HMOX1
* 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 HMOX1 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 # 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)

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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=26)
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
chr22:35782975-35782975p.K148E2
chr22:35782808-35782808p.D92G2
chr22:35789485-35789485p.R254T2
chr22:35783086-35783086p.R185S2
chr22:35783113-35783113p.A194T2
chr22:35782755-35782755p.F74F2
chr22:35779116-35779116p.S14*1
chr22:35783139-35783139p.E202D1
chr22:35782786-35782786p.R85C1
chr22:35789521-35789521p.P266L1

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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
# sample 2171   21 321  37 8
# mutation 2161   21 321  37 8
nonsynonymous SNV  141   21 21   15 4
synonymous SNV 2 2       111  22 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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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
chr22:35782808p.D92G2
chr22:35779123p.A16A1
chr22:35789509p.A151V1
chr22:35782827p.R262H1
chr22:35783086p.K18N1
chr22:35779129p.A151A1
chr22:35789515p.Q264L1
chr22:35782832p.I57I1
chr22:35783113p.L157L1
chr22:35782704p.L268L1

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 HMOX1 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 HMOX1

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

ADAP2,AQP9,CD163,CD300A,CD33,CD68,CRYBB1,
CTSL,FTL,GPR65,HMOX1,IFI30,LGMN,LILRB3,
NLRC4,NPL,PLIN2,S100Z,SIGLEC7,SIGLEC9,VSIG4
CCL18,CD163,CD200R1L,CDRT15,CEACAM3,CETP,CHST13,
GAD2,GAP43,HMOX1,LGI2,OR2AG1,OR8D1,RHOXF2B,
SLC48A1,SNORA19,SPATA8,SPRR2F,TECTB,VENTXP1,WNT1

CD14,CD300A,CD33,CD86,CYTH4,FCGR1A,FCGR1B,
FPR3,HAVCR2,HMOX1,LAIR1,LAPTM5,LRRC25,MS4A4A,
MS4A6A,NFAM1,SIGLEC7,SIGLEC9,SLCO2B1,SPI1,TYROBP
ACOX1,ACSL5,ANKS4B,ATP1B1,LINC00483,C1orf106,CHMP4B,
CTSZ,ESPN,FTH1P3,HECTD3,HKDC1,HMOX1,KALRN,
KIAA0247,MGAT4A,MPP5,PRR13,SLC9A3R1,TRHDE,TUBAL3
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 HMOX1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P09601; -.
ChemistryChEMBL CHEMBL2823; -.
Organism-specific databasesPharmGKB PA29341; -.
Organism-specific databasesCTD 3162; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00157heme oxygenase (decycling) 1approved; nutraceuticalNADH
DB01942heme oxygenase (decycling) 1experimentalFormic Acid
DB02073heme oxygenase (decycling) 1experimentalBiliverdine Ix Alpha
DB02468heme oxygenase (decycling) 1experimental12-Phenylheme
DB03014heme oxygenase (decycling) 1experimentalHeme
DB03906heme oxygenase (decycling) 1experimental2-Phenylheme
DB04803heme oxygenase (decycling) 1experimentalVerdoheme
DB06914heme oxygenase (decycling) 1experimental1-({2-[2-(4-CHLOROPHENYL)ETHYL]-1,3-DIOXOLAN-2-YL}METHYL)-1H-IMIDAZOLE
DB07342heme oxygenase (decycling) 1experimental1-(adamantan-1-yl)-2-(1H-imidazol-1-yl)ethanone


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Cross referenced IDs for HMOX1
* 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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