Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	HMOX1
	Gene name	heme oxygenase (decycling) 1
	Synonyms	HMOX1D\|HO-1\|HSP32\|bK286B10
	Cytomap	UCSC genome browser: 22q13.1
	Genomic location	chr22 :35777059-35790207
	Type of gene	protein-coding
	RefGenes	NM_002133.2,
	Ensembl id	ENSG00000100292
	Description	heat shock protein, 32-kDheme oxygenase 1
	Modification date	20141222
dbXrefs	MIM : 141250
	HGNC : HGNC
	Ensembl : ENSG00000100292
	HPRD : 00782
	Vega : OTTHUMG00000150960
Protein	UniProt: P09601 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_HMOX1
	BioGPS: 3162
	Gene Expression Atlas: ENSG00000100292
	The Human Protein Atlas: ENSG00000100292
Pathway	NCI Pathway Interaction Database: HMOX1
	KEGG: HMOX1
	REACTOME: HMOX1
	ConsensusPathDB
	Pathway Commons: HMOX1
Metabolism	MetaCyc: HMOX1
	HUMANCyc: HMOX1
Regulation	Ensembl's Regulation: ENSG00000100292
	miRBase: chr22 :35,777,059-35,790,207
	TargetScan: NM_002133
	cisRED: ENSG00000100292
Context	iHOP: HMOX1
	cancer metabolism search in PubMed: HMOX1
	UCL Cancer Institute: HMOX1
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of HMOX1 in cancer cell metabolism	1. 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)

Cancer 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/

Metabolic Pathway Description
KEGG_PORPHYRIN_AND_CHLOROPHYLL_METABOLISM REACTOME_METABOLISM_OF_PORPHYRINS

Others
OMIM	141250; gene. 614034; phenotype.
Orphanet
Disease	KEGG Disease: HMOX1
	MedGen: HMOX1 (Human Medical Genetics with Condition)
	ClinVar: HMOX1
Phenotype	MGI: HMOX1 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

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

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows HMOX1 related fusion information.

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

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

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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SNV 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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Somatic 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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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
chr22:35783113-35783113	p.A194T	2
chr22:35782755-35782755	p.F74F	2
chr22:35782975-35782975	p.K148E	2
chr22:35782808-35782808	p.D92G	2
chr22:35789485-35789485	p.R254T	2
chr22:35783086-35783086	p.R185S	2
chr22:35789509-35789509	p.R262H	1
chr22:35782948-35782948	p.G139C	1
chr22:35783130-35783130	p.V199V	1
chr22:35782760-35782760	p.P76H	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample		2	1	7	1				2	1		3	2	1			3	7		8
# mutation		2	1	6	1				2	1		3	2	1			3	7		8
nonsynonymous SNV			1	4	1				2	1		2	1				1	5		4
synonymous SNV		2		2								1	1	1			2	2		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
chr22:35782808	p.D92G	2
chr22:35789491	p.Y114Y	1
chr22:35782809	p.K256R	1
chr22:35783051	p.R123C	1
chr22:35789496	p.P258T	1
chr22:35782824	p.A151V	1
chr22:35783055	p.R262H	1
chr22:35789509	p.A16A	1
chr22:35779123	p.A151A	1
chr22:35782827	p.Q264L	1

Other 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

Copy 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

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.

: Open all plots for all cancer types

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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

: 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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P09601; -.
Chemistry	ChEMBL	CHEMBL2823; -.
Organism-specific databases	PharmGKB	PA29341; -.
Organism-specific databases	CTD	3162; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00157	heme oxygenase (decycling) 1	approved; nutraceutical	NADH
DB01942	heme oxygenase (decycling) 1	experimental	Formic Acid
DB02073	heme oxygenase (decycling) 1	experimental	Biliverdine Ix Alpha
DB02468	heme oxygenase (decycling) 1	experimental	12-Phenylheme
DB03014	heme oxygenase (decycling) 1	experimental	Heme
DB03906	heme oxygenase (decycling) 1	experimental	2-Phenylheme
DB04803	heme oxygenase (decycling) 1	experimental	Verdoheme
DB06914	heme oxygenase (decycling) 1	experimental	1-({2-[2-(4-CHLOROPHENYL)ETHYL]-1,3-DIOXOLAN-2-YL}METHYL)-1H-IMIDAZOLE
DB07342	heme oxygenase (decycling) 1	experimental	1-(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