Browse OMD

Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Secreted, extracellular space, extracellular matrix
Domain PF13855 Leucine rich repeat
Function

May be implicated in biomineralization processes. Has a function in binding of osteoblasts via the alpha(V)beta(3)-integrin (By similarity).

> Gene Ontology
 
Biological Process GO:0001503 ossification
GO:0006022 aminoglycan metabolic process
GO:0006023 aminoglycan biosynthetic process
GO:0006024 glycosaminoglycan biosynthetic process
GO:0006026 aminoglycan catabolic process
GO:0006027 glycosaminoglycan catabolic process
GO:0006790 sulfur compound metabolic process
GO:0018146 keratan sulfate biosynthetic process
GO:0030203 glycosaminoglycan metabolic process
GO:0030278 regulation of ossification
GO:0030282 bone mineralization
GO:0030500 regulation of bone mineralization
GO:0031214 biomineral tissue development
GO:0042339 keratan sulfate metabolic process
GO:0042340 keratan sulfate catabolic process
GO:0044272 sulfur compound biosynthetic process
GO:0044273 sulfur compound catabolic process
GO:0070167 regulation of biomineral tissue development
GO:1901136 carbohydrate derivative catabolic process
GO:1901565 organonitrogen compound catabolic process
GO:1903510 mucopolysaccharide metabolic process
Molecular Function -
Cellular Component GO:0005578 proteinaceous extracellular matrix
GO:0005775 vacuolar lumen
GO:0005796 Golgi lumen
GO:0043202 lysosomal lumen
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-3656244: Defective B4GALT1 causes B4GALT1-CDG (CDG-2d)
R-HSA-3656225: Defective CHST6 causes MCDC1
R-HSA-3656243: Defective ST3GAL3 causes MCT12 and EIEE15
R-HSA-1643685: Disease
R-HSA-3560782: Diseases associated with glycosaminoglycan metabolism
R-HSA-3781865: Diseases of glycosylation
R-HSA-1630316: Glycosaminoglycan metabolism
R-HSA-2022854: Keratan sulfate biosynthesis
R-HSA-2022857: Keratan sulfate degradation
R-HSA-1638074: Keratan sulfate/keratin metabolism
R-HSA-1430728: Metabolism
R-HSA-71387: Metabolism of carbohydrates
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between OMD and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.

Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of OMD in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of OMD in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-1.3270.00898
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.9650.279
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-1.5860.0256
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.8250.117
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.6990.638
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-0.9870.573
729033130MelanomaallAnti-PD-1 (nivolumab) 2623-0.490.576
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 1511-0.1730.888
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-1.1130.416
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.3180.797
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 281.2570.426
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 68230-0.7930.048
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of OMD in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 27733.703.70.27
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27593.703.70.314
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of OMD. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of OMD. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by OMD.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of OMD. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of OMD expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between OMD and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolOMD
Nameosteomodulin
Aliases osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location9q22.31
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting OMD collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.