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 OMD
Basic gene info.Gene symbolOMD
Gene nameosteomodulin
SynonymsOSAD|SLRR2C
CytomapUCSC genome browser: 9q22.31
Genomic locationchr9 :95176526-95186836
Type of geneprotein-coding
RefGenesNM_005014.2,
Ensembl idENSG00000127083
DescriptionKSPG osteomodulinkeratan sulfate proteoglycan osteomodulinosteoadherin proteoglycan
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000127083
HPRD : 10128
Vega : OTTHUMG00000020225
ProteinUniProt: Q99983
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_OMD
BioGPS: 4958
Gene Expression Atlas: ENSG00000127083
The Human Protein Atlas: ENSG00000127083
PathwayNCI Pathway Interaction Database: OMD
KEGG: OMD
REACTOME: OMD
ConsensusPathDB
Pathway Commons: OMD
MetabolismMetaCyc: OMD
HUMANCyc: OMD
RegulationEnsembl's Regulation: ENSG00000127083
miRBase: chr9 :95,176,526-95,186,836
TargetScan: NM_005014
cisRED: ENSG00000127083
ContextiHOP: OMD
cancer metabolism search in PubMed: OMD
UCL Cancer Institute: OMD
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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

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

Mutations for OMD
* 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 OMD 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
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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=13)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr9:95179145-95179145p.P232P6
chr9:95179820-95179820p.I7I3
chr9:95179557-95179557p.Q95R2
chr9:95177603-95177603p.R366Q2
chr9:95177478-95177478p.A408S2
chr9:95177716-95177716p.H328H2
chr9:95179207-95179207p.E212K1
chr9:95177580-95177580p.Q374E1
chr9:95179512-95179512p.S110*1
chr9:95179006-95179006p.L279I1

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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=7

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   16  2 2  3 3  22 6
# mutation   10  2 2  3 3  22 6
nonsynonymous SNV   8  2 2  2 3  22 5
synonymous SNV   2       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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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
chr9:95179145p.P232P6
chr9:95179820p.I7I3
chr9:95179731p.L279I1
chr9:95177651p.H92Y1
chr9:95179221p.F253F1
chr9:95177694p.G52R1
chr9:95179223p.D37G1
chr9:95178974p.P232H1
chr9:95179237p.P228L1
chr9:95179006p.P228S1

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 OMD 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 OMD

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

ASPN,CDH11,COL5A2,COL8A2,DCN,ECM2,FAM26E,
FBN1,GALNT15,GLT8D2,GPR1,GXYLT2,ITGBL1,LRRC15,
LUM,MXRA5,OMD,PDGFRL,RASGRF2,RECK,SGCD
ACKR4___CX3CR1,CLIC2,CYBRD1,DCN,DKK2,DPYSL3,FBLN1,
FGL2,GALNT12,MFAP4,NEGR1,NT5E,OGN,OLFML1,
OMD,PAM,PDGFRL,PTGFR,RECK,TIMP2,UST

ASPN,C1QTNF3,CILP,CNTN4,DCN,DIO2,ECM2,
EFEMP1,FGF14,HMCN1,ITGBL1,LHFP,MGP,NOX4,
OLFML2B,OMD,PODN,PRICKLE1,SFRP2,SSPN,TGFB3
C1QTNF3,CAV2,CHRDL1,CTSF,DCN,ETNK2,GALNT11,
GNG11,LEPR,LHFP,OGN,OMD,SDC2,SPG20,
TAF9B,SLC35G2,TRPC1,TWSG1,UST,WASF3,ZNF781
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 OMD


There's no related Drug.
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Cross referenced IDs for OMD
* 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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