TISIDB

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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 [ TOP ]
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 [ TOP ]
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 [ TOP ]
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

> KEGG and Reactome Pathway

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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
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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 [ TOP ]
There is no record.

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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

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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
29301958	CRISPR-Cas9	melanoma	B16F10	Pmel-1 T cell	NA/NS	NA/NS
29301958	CRISPR-Cas9	melanoma	B16F10	OT-1 T cell	NA/NS	NA/NS
28783722	CRISPR-Cas9	melanoma	Mel624	2CT-CRISPR	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX+Anti-PD1	NA/NS	NA/NS
28723893	CRISPR-Cas9	melanoma	B16	GVAX	NA/NS	NA/NS
25691366	RNAi	Breast cancer	MCF7	Luc-CTL assay	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Primary screen	NA/NS	NA/NS
24476824	shRNA	melanoma	B16	Secondary screen	NA/NS	NA/NS

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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

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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
1	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	14	12	-1.327	0.00898
2	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	6	5	-0.965	0.279
3	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	7	-1.586	0.0256
4	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	-0.825	0.117
5	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	-0.699	0.638
6	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	-0.987	0.573
7	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	26	23	-0.49	0.576
8	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	15	11	-0.173	0.888
9	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	11	12	-1.113	0.416
10	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	4	8	0.318	0.797
11	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	2	0	0	1
12	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	2	8	1.257	0.426
13	29443960	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	68	230	-0.793	0.048

> Mutation difference between responders and non-responders

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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	% Diff (R vs NR)	Pval
1	25765070	Non-small cell lung cancer (NSCLC)	all	Anti-PD-1 (pembrolizumab)	14	17	0	0	1
2	25765070	Non-small cell lung cancer (NSCLC)	smoking	Anti-PD-1 (pembrolizumab)	10	3	0	0	1
3	25765070	Non-small cell lung cancer (NSCLC)	non-smoking	Anti-PD-1 (pembrolizumab)	4	14	0	0	1
4	26359337	Melanoma	all	Anti-CTLA-4 (ipilimumab)	27	73	3.7	3.7	0.27
5	26359337	Melanoma	BRAFi	Anti-CTLA-4 (ipilimumab)	0	14	0	0	1
6	26359337	Melanoma	non-BRAFi	Anti-CTLA-4 (ipilimumab)	27	59	3.7	3.7	0.314
7	26997480	Melanoma	all	Anti-PD-1 (pembrolizumab and nivolumab)	21	17	0	0	1
8	26997480	Melanoma	MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	8	6	0	0	1
9	26997480	Melanoma	non-MAPKi	Anti-PD-1 (pembrolizumab and nivolumab)	13	11	0	0	1
10	28552987	Urothelial cancer	all	Anti-PD-L1 (atezolizumab)	9	16	0	0	1
11	28552987	Urothelial cancer	smoking	Anti-PD-L1 (atezolizumab)	5	9	0	0	1
12	28552987	Urothelial cancer	non-smoking	Anti-PD-L1 (atezolizumab)	4	7	0	0	1
13	29033130	Melanoma	all	Anti-PD-1 (nivolumab)	38	27	0	0	1
14	29033130	Melanoma	NIV3-PROG	Anti-PD-1 (nivolumab)	22	13	0	0	1
15	29033130	Melanoma	NIV3-NAIVE	Anti-PD-1 (nivolumab)	16	14	0	0	1
16	29301960	Clear cell renal cell carcinoma (ccRCC)	all	Anti-PD-1 (nivolumab)	11	13	0	0	1
17	29301960	Clear cell renal cell carcinoma (ccRCC)	VEGFRi	Anti-PD-1 (nivolumab)	6	1	0	0	1
18	29301960	Clear cell renal cell carcinoma (ccRCC)	non-VEGFRi	Anti-PD-1 (nivolumab)	5	12	0	0	1

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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 [ TOP ]

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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 [ TOP ]

> Immunostimulator [ TOP ]

> MHC molecule [ TOP ]

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
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 [ TOP ]

> Receptor [ TOP ]

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Distribution of OMD expression across immune and molecular subtypes. > Immune subtype > Molecular subtype

> Immune subtype [ TOP ]

> Molecular subtype [ TOP ]

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Associations between OMD and clinical features. > Overall survival analysis > Cancer stage > Tumor grade

> Overall survival [ TOP ]

> Stage [ TOP ]

> Grade [ TOP ]

Summary
Symbol	OMD
Name	osteomodulin
Aliases	osteoadherin; SLRR2C; osteoadherin proteoglycan; OSAD; KSPG osteomodulin; keratan sulfate proteoglycan osteo ......
Chromosomal Location	9q22.31
External Links	HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content	Drugs targeting OMD collected from DrugBank database.

> Drugs from DrugBank database [ TOP ]
There is no record.

Browse OMD