Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. Dr. Rajesh Raju obtained his Ph.D. in Biotechnology from the Institute of Bioinformatics (IOB), Bangalore and the Kuvempu University, Shivamogga. Resources for gene-centric single sample Gene Set Enrichment Analysis (ssGSEA) of gene expression data (e.g. Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. Proteomics 2004, 4, 1551-1561 DOI 10.1002/pmic.200300772 1551 PhosphoSite: A bioinformatics resource dedicated to physiological protein phosphorylation Peter V. Hornbeck1, Indy Chabra2, Jon M. Kornhauser1, Elzbieta Skrzypek1 and Bin Zhang1 1 Cell Signaling Technology, Beverly, MA, USA 2 ForScience Inc., Stony Brook, NY, USA PhosphoSite is a curated, web-based bioinformatics resource . Krug K et al (2018) A curated resource for phosphosite-specific signature analysis. However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of . . PTMsigDB consists of modification site specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications, which provides the foundation to perform PTM signature enrichment analysis. The three journals most represented in PSP are the Journal of Biological Chemistry, Molecular and Cellular . However, pathway analysis of PTM datasets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level due to the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. A curated resource for phosphosite-specific signature analysis, Molecular & Cellular Proteomics (in Press). Make the most of your business, using electronic signature solutions by signNow. such as phosphorylation. Curation and maintenance of such a database requires knowledge from domain experts, which in this study are represented by curators from PhosphoSitePlus, NetPath and WikiPathways. However, practical tools for studying the signatures of . Pathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of . Krug K(1), Mertins P(1)(2)(3), Zhang B(4), Hornbeck P(4), Raju R(5), Ahmad . PSP integrates both low- and high-throughput (LTP and HTP) data sources into a single reliable and comprehensive resource.Nearly 10,000 journal articles , including both LTP and HTP reports, have been manually curated by expert scientists from over 480 different journals since 2001. Molecular & Cellular Proteomics 18 (3), 576-593 , 2019 PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. A Curated Resource for Phosphosite-specific Signature Analysis. Author summary Genomic DNA alteration signatures are recurring genomic patterns that are the imprints of mutagenic processes accumulated over the lifetime of cancer cell. ssGSEA2./PTM-SEA.
Although PTMsigDB enables kinase signature analysis similar to published tools described above, it additionally includes many curated signature sets of PTM sites mined from Phos . An example of connectivity analysis for a user provided input L1000 signature (of a multi-targeted kinase inhibitor midostaurin) is shown in Figure 4, with other strongly concordant or discordant LINCS signatures connected by edges in the circos plot.
Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. In addition, the resource contains a variety of secondary analysis tools that allow the researcher to calculate epitope conservation, population coverage, and other relevant analytic variables. [PMID: 30563849] Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, Matthew Szucs, Filip Mundt, Dominique Forestier, Judit Jane-Valbuena, Hasmik Keshishian, Michael A Gillette, Pablo Tamayo, Jill P Mesirov, Jacob D Jaffe, Steven A Carr, D R Mani . Methods for mapping proteomics data on 3D protein structure. A curated resource for phosphosite-specific signature analysis, Molecular & Cellular Proteomics (in Press). . .
A curated resource for phosphosite-specific signature analysis Karsten Krug 1 , Philipp Mertins 1,2,3 , Bin Zhang 4 , Peter Hornbeck 4 , Rajesh Raju 5 , Rushdy Ahmad 1 , Apache-2.0 license 14 stars 1 fork
Mol Cell Proteomics. Application of PTM-SEA to . GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. A Curated Resource for Phosphosite-specific Signature Analysis. | Find, read and cite all the research you need on ResearchGate Article PDF Available A Curated Resource for Phosphosite-specific Signature Analysis Here we present the first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications. The web use is free for everyone including commercial. Copy number alteration is a key driver for the progression of multiple cancer, including prostate cancer, which is particularly driven by complex genome alterations. Protein, Sequence, or Reference Search: Protein Searches retrieve lists of proteins and their modification types . This curated resource was then used to perform phosphosite-specific signature analysis for MS-based . A Curated Resource for Phosphosite-specific Signature Analysis.
A Curated Resource for Phosphosite-specific Signature Analysis Authors Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, . At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). The first version of PTMsigDB is presented, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications, and outperformed gene-centric analysis in detection of EGF induced phospho signaling events.
. Signature resources. PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. Clicking on a publication, gene or gene signature will open up a data type-specific view for each of these. A Curated Resource for Phosphosite-specific Signature Analysis. A curated resource for phosphosite-specific signature analysis K Krug, P Mertins, B Zhang, P Hornbeck, R Raju, R Ahmad, M Szucs, . 2019; 18(3):576-593 (ISSN: 1535-9484) Krug K; Mertins P; Zhang B; Hornbeck P; Raju R; Ahmad R; Szucs M; Mundt F; Forestier D; Jane-Valbuena J; Keshishian H; Gillette MA; Tamayo P; Mesirov JP; Jaffe JD; Carr SA; Mani DR The publication view provides information about the published article, its authors, an abstract and a list of gene signatures associated . Mol Cell Proteom. The survival analysis of the optimal gene signature showed that there was a significant difference between the high-risk group and the low-risk group (p < 0.0001) . PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. We describe an approach to perform phosphosite-specific signature analysis (PTM-SEA) based on a curated database of phosphosite-specific signatures (PTMsigDB). We have developed a PTM signatures database (PTMsigDB) providing curated phosphorylation signatures of kinases, perturbations and signaling pathways to enable site-specific PTM signature enrichment analysis (PTM-SEA). PTM-Signature Enrichment Analysis (PMT-SEA) is a modified version of ssGSEA to perform site-specific signature analysis by scoring PTMsigDB's bi-directional signature-sets. PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. . The first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications is presented, enabling PTMSignature Enrichment Analysis (PTM-SEA) of quantitative MS data. The primary purpose of this repository is to supplement our manuscript in which we describe . However, pathway analysis of PTM data sets. To learn more about the scope of PhosphoSitePlus , click here. A Curated Resource for Phosphosite-specific Signature . We adapted the widely used single sample Gene Set Enrichment Analysis approach to utilize PTMsigDB, enabling PTM S ignature E nrichment A nalysis . Pathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases. We have developed a PTM signa- tures database (PTMsigDB) pro- viding curated phosphorylation signatures of kinases, perturba- tions and signaling pathways to enable site-specific PTM signa- ture enrichment analysis (PTM- SEA). PhosphoSitePlus provides comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, acetylation, and more. However, pathway . Abstract. Mol Cell Proteomics.
However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic . Item Type: Article: Title: A curated resource for phosphosite-specific signature analysis: Creators Name: Krug, K. and Mertins, P. and Zhang, B. and Hornbeck, P. and . Dec 18, 2018 - A Curated Resource for Phosphosite-specific Signature Analysis. At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). mRNAs, proteins) and site-centric PTM Signature Enrichment Analysis (PTM-SEA) [1] of phosphoproteomics data sets using the PTM signatures database (PTMsigDB) [1].. Disclaimer. He has been leading the IOB's efforts in the development and analysis of signaling pathways available through NetPath, a resource of signaling pathways. PTM-Signature Enrichment Analysis (PMT-SEA) is a modified version of ssGSEA to perform site-specific signature analysis by scoring PTMsigDB's bi-directional signature-sets. This page summarizes selected information from the record referenced above and curated into PhosphoSitePlus , a comprehensive online resource for the study of protein post-translational modifications (NAR, 2015, 43:D512-20). Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. Application of PTM-SEA to phosphoproteomes of several cell lines perturbed with growth factors, cell cycle inhibitors . Note that other related kinase inhibitors are identified, suggesting overlapping kinase targets.
Although PTMsigDB enables kinase signature analysis similar to published tools described above, it additionally includes many curated signature sets of PTM sites mined from Phos . An example of connectivity analysis for a user provided input L1000 signature (of a multi-targeted kinase inhibitor midostaurin) is shown in Figure 4, with other strongly concordant or discordant LINCS signatures connected by edges in the circos plot.
Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic tools that leverage PTM site-specific information. In addition, the resource contains a variety of secondary analysis tools that allow the researcher to calculate epitope conservation, population coverage, and other relevant analytic variables. [PMID: 30563849] Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, Matthew Szucs, Filip Mundt, Dominique Forestier, Judit Jane-Valbuena, Hasmik Keshishian, Michael A Gillette, Pablo Tamayo, Jill P Mesirov, Jacob D Jaffe, Steven A Carr, D R Mani . Methods for mapping proteomics data on 3D protein structure. A curated resource for phosphosite-specific signature analysis, Molecular & Cellular Proteomics (in Press). . .
A curated resource for phosphosite-specific signature analysis Karsten Krug 1 , Philipp Mertins 1,2,3 , Bin Zhang 4 , Peter Hornbeck 4 , Rajesh Raju 5 , Rushdy Ahmad 1 , Apache-2.0 license 14 stars 1 fork
Mol Cell Proteomics. Application of PTM-SEA to . GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. A Curated Resource for Phosphosite-specific Signature Analysis. | Find, read and cite all the research you need on ResearchGate Article PDF Available A Curated Resource for Phosphosite-specific Signature Analysis Here we present the first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications. The web use is free for everyone including commercial. Copy number alteration is a key driver for the progression of multiple cancer, including prostate cancer, which is particularly driven by complex genome alterations. Protein, Sequence, or Reference Search: Protein Searches retrieve lists of proteins and their modification types . This curated resource was then used to perform phosphosite-specific signature analysis for MS-based . A Curated Resource for Phosphosite-specific Signature Analysis.
A Curated Resource for Phosphosite-specific Signature Analysis Authors Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, . At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). The first version of PTMsigDB is presented, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications, and outperformed gene-centric analysis in detection of EGF induced phospho signaling events.
. Signature resources. PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. Clicking on a publication, gene or gene signature will open up a data type-specific view for each of these. A Curated Resource for Phosphosite-specific Signature Analysis. A curated resource for phosphosite-specific signature analysis K Krug, P Mertins, B Zhang, P Hornbeck, R Raju, R Ahmad, M Szucs, . 2019; 18(3):576-593 (ISSN: 1535-9484) Krug K; Mertins P; Zhang B; Hornbeck P; Raju R; Ahmad R; Szucs M; Mundt F; Forestier D; Jane-Valbuena J; Keshishian H; Gillette MA; Tamayo P; Mesirov JP; Jaffe JD; Carr SA; Mani DR The publication view provides information about the published article, its authors, an abstract and a list of gene signatures associated . Mol Cell Proteom. The survival analysis of the optimal gene signature showed that there was a significant difference between the high-risk group and the low-risk group (p < 0.0001) . PhosphoSite provides information about the phosphorylated residue and its surrounding sequence, orthologous sites in other species, location of the site within known domains and motifs, and relevant literature references. We describe an approach to perform phosphosite-specific signature analysis (PTM-SEA) based on a curated database of phosphosite-specific signatures (PTMsigDB). We have developed a PTM signatures database (PTMsigDB) providing curated phosphorylation signatures of kinases, perturbations and signaling pathways to enable site-specific PTM signature enrichment analysis (PTM-SEA). PTM-Signature Enrichment Analysis (PMT-SEA) is a modified version of ssGSEA to perform site-specific signature analysis by scoring PTMsigDB's bi-directional signature-sets. PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. . The first version of PTMsigDB, a database of modification site-specific signatures of perturbations, kinase activities and signaling pathways curated from more than 2,500 publications is presented, enabling PTMSignature Enrichment Analysis (PTM-SEA) of quantitative MS data. The primary purpose of this repository is to supplement our manuscript in which we describe . However, pathway analysis of PTM data sets. To learn more about the scope of PhosphoSitePlus , click here. A Curated Resource for Phosphosite-specific Signature . We adapted the widely used single sample Gene Set Enrichment Analysis approach to utilize PTMsigDB, enabling PTM S ignature E nrichment A nalysis . Pathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases. We have developed a PTM signa- tures database (PTMsigDB) pro- viding curated phosphorylation signatures of kinases, perturba- tions and signaling pathways to enable site-specific PTM signa- ture enrichment analysis (PTM- SEA). PhosphoSitePlus provides comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, acetylation, and more. However, pathway . Abstract. Mol Cell Proteomics.
However, pathway analysis of PTM data sets generated by mass spectrometry (MS)-based proteomics is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases and bioinformatic . Item Type: Article: Title: A curated resource for phosphosite-specific signature analysis: Creators Name: Krug, K. and Mertins, P. and Zhang, B. and Hornbeck, P. and . Dec 18, 2018 - A Curated Resource for Phosphosite-specific Signature Analysis. At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). mRNAs, proteins) and site-centric PTM Signature Enrichment Analysis (PTM-SEA) [1] of phosphoproteomics data sets using the PTM signatures database (PTMsigDB) [1].. Disclaimer. He has been leading the IOB's efforts in the development and analysis of signaling pathways available through NetPath, a resource of signaling pathways. PTM-Signature Enrichment Analysis (PMT-SEA) is a modified version of ssGSEA to perform site-specific signature analysis by scoring PTMsigDB's bi-directional signature-sets. This page summarizes selected information from the record referenced above and curated into PhosphoSitePlus , a comprehensive online resource for the study of protein post-translational modifications (NAR, 2015, 43:D512-20). Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. Application of PTM-SEA to phosphoproteomes of several cell lines perturbed with growth factors, cell cycle inhibitors . Note that other related kinase inhibitors are identified, suggesting overlapping kinase targets.