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 ODC1
Basic gene info.Gene symbolODC1
Gene nameornithine decarboxylase 1
SynonymsODC
CytomapUCSC genome browser: 2p25
Genomic locationchr2 :10580507-10588453
Type of geneprotein-coding
RefGenesNM_001287188.1,
NM_001287189.1,NM_001287190.1,NM_002539.2,
Ensembl idENSG00000115758
Descriptionornithine decarboxylase
Modification date20141207
dbXrefs MIM : 165640
HGNC : HGNC
Ensembl : ENSG00000115758
HPRD : 01324
Vega : OTTHUMG00000090450
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_ODC1
BioGPS: 4953
Gene Expression Atlas: ENSG00000115758
The Human Protein Atlas: ENSG00000115758
PathwayNCI Pathway Interaction Database: ODC1
KEGG: ODC1
REACTOME: ODC1
ConsensusPathDB
Pathway Commons: ODC1
MetabolismMetaCyc: ODC1
HUMANCyc: ODC1
RegulationEnsembl's Regulation: ENSG00000115758
miRBase: chr2 :10,580,507-10,588,453
TargetScan: NM_001287188
cisRED: ENSG00000115758
ContextiHOP: ODC1
cancer metabolism search in PubMed: ODC1
UCL Cancer Institute: ODC1
Assigned class in ccmGDBC

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Phenotypic Information for ODC1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
KEGG_ARGININE_AND_PROLINE_METABOLISM
KEGG_GLUTATHIONE_METABOLISM
REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES
REACTOME_METABOLISM_OF_POLYAMINES

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: ODC1
MedGen: ODC1 (Human Medical Genetics with Condition)
ClinVar: ODC1
PhenotypeMGI: ODC1 (International Mouse Phenotyping Consortium)
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.

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 ODC1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF081601PPP3CB18408107522735775230966ODC140468021058362810584299
BG282567KITLG11475128888742888887893ODC146851921058051410580565
BM794694ODC136921058215910582225ODC16666621058076310582178

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=3

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check002.gifSomatic 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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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
chr2:10585130-10585130p.D10G3
chr2:10581690-10581690p.T396A3
chr2:10583952-10583952p.R154W2
chr2:10585138-10585138p.E7D2
chr2:10581645-10581645p.G411R2
chr2:10580869-10580869p.S456L2
chr2:10584677-10584677p.A67T1
chr2:10581771-10581771p.R369C1
chr2:10582278-10582278p.A258E1
chr2:10580951-10580951p.V429I1

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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
# sample11110  1 1  321  45 3
# mutation1119  1 1  421  45 3
nonsynonymous SNV1 15  1 1  111  34 2
synonymous SNV 1 4       31   11 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
chr2:10585130p.D10G,ODC13
chr2:10582260p.P135L,ODC12
chr2:10585139p.S327L,ODC11
chr2:10580867p.A129A,ODC11
chr2:10582006p.S311Y,ODC11
chr2:10583844p.V89V,ODC11
chr2:10580869p.V300I,ODC11
chr2:10582007p.C88F,ODC11
chr2:10583902p.E299K,ODC11
chr2:10580917p.S84C,ODC11

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 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

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

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
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 ODC1
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00114ornithine decarboxylase 1nutraceuticalPyridoxal Phosphate
DB00127ornithine decarboxylase 1approved; nutraceuticalSpermine
DB01917ornithine decarboxylase 1experimentalPutrescine
DB02209ornithine decarboxylase 1experimentalPyridoxine-5'-Phosphate
DB02824ornithine decarboxylase 1experimentalN-Pyridoxyl-Glycine-5-Monophosphate
DB03856ornithine decarboxylase 1experimentalAlpha-Difluoromethylornithine
DB04083ornithine decarboxylase 1experimentalN'-Pyridoxyl-Lysine-5'-Monophosphate
DB04263ornithine decarboxylase 1experimentalG418
DB00125ornithine decarboxylase 1approved; nutraceuticalL-Arginine
DB03904ornithine decarboxylase 1experimentalUrea
DB00134ornithine decarboxylase 1approved; nutraceuticalL-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



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