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 ODC1

Basic gene info.	Gene symbol	ODC1
	Gene name	ornithine decarboxylase 1
	Synonyms	ODC
	Cytomap	UCSC genome browser: 2p25
	Genomic location	chr2 :10580507-10588453
	Type of gene	protein-coding
	RefGenes	NM_001287188.1, NM_001287189.1,NM_001287190.1,NM_002539.2,
	Ensembl id	ENSG00000115758
	Description	ornithine decarboxylase
	Modification date	20141207
dbXrefs	MIM : 165640
	HGNC : HGNC
	Ensembl : ENSG00000115758
	HPRD : 01324
	Vega : OTTHUMG00000090450
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_ODC1
	BioGPS: 4953
	Gene Expression Atlas: ENSG00000115758
	The Human Protein Atlas: ENSG00000115758
Pathway	NCI Pathway Interaction Database: ODC1
	KEGG: ODC1
	REACTOME: ODC1
	ConsensusPathDB
	Pathway Commons: ODC1
Metabolism	MetaCyc: ODC1
	HUMANCyc: ODC1
Regulation	Ensembl's Regulation: ENSG00000115758
	miRBase: chr2 :10,580,507-10,588,453
	TargetScan: NM_001287188
	cisRED: ENSG00000115758
Context	iHOP: ODC1
	cancer metabolism search in PubMed: ODC1
	UCL Cancer Institute: ODC1
Assigned class in ccmGDB	C

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Phenotypic Information for ODC1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: ODC1
	Familial Cancer Database: ODC1

* 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_ARGININE_AND_PROLINE_METABOLISM KEGG_GLUTATHIONE_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_POLYAMINES

Others
OMIM
Orphanet
Disease	KEGG Disease: ODC1
	MedGen: ODC1 (Human Medical Genetics with Condition)
	ClinVar: ODC1
Phenotype	MGI: ODC1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: ODC1

Mutations for ODC1

* 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 ODC1 related fusion information.

ID	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
BF081601	PPP3CB	18	408	10	75227357	75230966	ODC1	404	680	2	10583628	10584299
BG282567	KITLG	11	475	12	88887428	88887893	ODC1	468	519	2	10580514	10580565
BM794694	ODC1	3	69	2	10582159	10582225	ODC1	66	666	2	10580763	10582178

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

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

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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=28)	Stat. for Synonymous SNVs (# total SNVs=13)

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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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
chr2:10581690-10581690	p.T396A	3
chr2:10585130-10585130	p.D10G	3
chr2:10581645-10581645	p.G411R	2
chr2:10580869-10580869	p.S456L	2
chr2:10583952-10583952	p.R154W	2
chr2:10585138-10585138	p.E7D	2
chr2:10582162-10582162	p.L297L	1
chr2:10585139-10585139	p.E7G	1
chr2:10583844-10583844	p.D190N	1
chr2:10584354-10584354	p.E106*	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	1	1	1	10			1		1			3	2	1			4	5		3
# mutation	1	1	1	9			1		1			4	2	1			4	5		3
nonsynonymous SNV	1		1	5			1		1			1	1	1			3	4		2
synonymous SNV		1		4								3	1				1	1		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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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
chr2:10585130	p.D10G,ODC1	3
chr2:10582260	p.P135L,ODC1	2
chr2:10583628	p.Y194C,ODC1	1
chr2:10584717	p.M1I,ODC1	1
chr2:10581771	p.G192G,ODC1	1
chr2:10583632	p.N71K,ODC1	1
chr2:10584768	p.G192D,ODC1	1
chr2:10581946	p.A67T,ODC1	1
chr2:10583644	p.D176D,ODC1	1
chr2:10582001	p.L53L,ODC1	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 ODC1 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 ODC1

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


B3GNT5,ASUN,CDC25A,CDCA8,CPSF3,DDX1,GOLT1B, KLF11,LDHB,LRRC8D,NOL10,ODC1,ORC1,PDIA6, PRPF38A,RAD54L,RNASEH1,SERBP1,SUV39H2,YWHAQ,ZNF695	CMC2,RUNX1-IT1,MALSU1,CLDN6,COPS3,DCUN1D5,EIF1, EIF1B,HOPX,HSPA8,IL31RA,LOC84740,MAP2K3,MLF1, MRPL1,NFATC1,ODC1,RRAGA,SLC25A3,TPT1,WDR77

BIRC5,CCT2,CCT7,CDK4,DTYMK,EPR1,GMNN, MAD2L1,MRPL30,MRPS12,NME1,ODC1,PNO1,POLR2D, PPIL1,PRMT1,PSMD14,RRM2,SRSF3,SRSF7,SNRPG	AEN,BYSL,DDX21,EXOSC9,GNL2,GPATCH4,GPR3, GTPBP4,LYAR,MAK16,NIFK,NOP16,NOP2,ODC1, PIGW,PNPT1,POLD3,RRS1,SRSF2,SRSF7,TRMT6

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 ODC1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB00114	ornithine decarboxylase 1	nutraceutical	Pyridoxal Phosphate
DB00127	ornithine decarboxylase 1	approved; nutraceutical	Spermine
DB01917	ornithine decarboxylase 1	experimental	Putrescine
DB02209	ornithine decarboxylase 1	experimental	Pyridoxine-5'-Phosphate
DB02824	ornithine decarboxylase 1	experimental	N-Pyridoxyl-Glycine-5-Monophosphate
DB03856	ornithine decarboxylase 1	experimental	Alpha-Difluoromethylornithine
DB04083	ornithine decarboxylase 1	experimental	N'-Pyridoxyl-Lysine-5'-Monophosphate
DB04263	ornithine decarboxylase 1	experimental	G418
DB00125	ornithine decarboxylase 1	approved; nutraceutical	L-Arginine
DB03904	ornithine decarboxylase 1	experimental	Urea
DB00134	ornithine decarboxylase 1	approved; nutraceutical	L-Methionine

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Cross referenced IDs for ODC1

* 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