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) . . However, pathway . Krug K(1), Mertins P(1)(2)(3), Zhang B(4), Hornbeck P(4), Raju R(5), Ahmad . Resources for gene-centric single sample Gene Set Enrichment Analysis (ssGSEA) of gene expression data (e.g. 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. Methods for mapping proteomics data on 3D protein structure. 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 . A curated resource for phosphosite-specific signature analysis, Molecular & Cellular Proteomics (in Press). 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 . Pathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of appropriately curated PTM signature databases. Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. A Curated Resource for Phosphosite-specific Signature . The three journals most represented in PSP are the Journal of Biological Chemistry, Molecular and Cellular . Application of PTM-SEA to phosphoproteomes of several cell lines perturbed with growth factors, cell cycle inhibitors . GeneSigDB: a manually curated database and resource for analysis of gene expression signatures. The publication view provides information about the published article, its authors, an abstract and a list of gene signatures associated . . 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, Molecular & Cellular Proteomics (in Press). Dec 18, 2018 - A Curated Resource for Phosphosite-specific Signature Analysis. A Curated Resource for Phosphosite-specific Signature Analysis. A Curated Resource for Phosphosite-specific Signature Analysis. 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. 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. 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. Pathway analysis of PTM data sets is typically performed at a gene-centric level because of the lack of . However, practical tools for studying the signatures of . . This curated resource was then used to perform phosphosite-specific signature analysis for MS-based . Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. . Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. A Curated Resource for Phosphosite-specific Signature Analysis. 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). 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). Signature resources. We adapted the widely used single sample Gene Set Enrichment Analysis approach to utilize PTMsigDB, enabling PTM S ignature E nrichment A nalysis . At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). Apache-2.0 license 14 stars 1 fork 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. 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). A curated resource for phosphosite-specific signature analysis K Krug, P Mertins, B Zhang, P Hornbeck, R Raju, R Ahmad, M Szucs, . Krug K et al (2018) A curated resource for phosphosite-specific signature analysis. 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. Protein, Sequence, or Reference Search: Protein Searches retrieve lists of proteins and their modification types . A Curated Resource for Phosphosite-specific Signature Analysis Authors Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, . . PhosphoSitePlus provides comprehensive information and tools for the study of protein post-translational modifications (PTMs) including phosphorylation, acetylation, and more. 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 , PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. The web use is free for everyone including commercial. At its launch it incorporated over 1200 journal articles identifying over 1200 non-redundant sites on over 500 human and mouse proteins ( Figure 1 ). A Curated Resource for Phosphosite-specific Signature Analysis. 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 . Dr. Rajesh Raju obtained his Ph.D. in Biotechnology from the Institute of Bioinformatics (IOB), Bangalore and the Kuvempu University, Shivamogga. Note that other related kinase inhibitors are identified, suggesting overlapping kinase targets. 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. PhosphoSite is populated with information derived from published literature as well as high-throughput discovery programs. 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 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. PhosphoSite , launched in 2003, was designed as a resource that would comprehensively aggregate information about the structure and regulatory interactions of phosphorylation sites. 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 . 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. 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. such as phosphorylation. ssGSEA2./PTM-SEA. To learn more about the scope of PhosphoSitePlus , click here. | Find, read and cite all the research you need on ResearchGate Article PDF Available A Curated Resource for Phosphosite-specific Signature Analysis However, pathway analysis of PTM data sets. The primary purpose of this repository is to supplement our manuscript in which we describe . We describe an approach to perform phosphosite-specific signature analysis (PTM-SEA) based on a curated database of phosphosite-specific signatures (PTMsigDB). Make the most of your business, using electronic signature solutions by signNow. Copy number alteration is a key driver for the progression of multiple cancer, including prostate cancer, which is particularly driven by complex genome alterations. 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 tools that leverage PTM site-specific information. mRNAs, proteins) and site-centric PTM Signature Enrichment Analysis (PTM-SEA) [1] of phosphoproteomics data sets using the PTM signatures database (PTMsigDB) [1].. Disclaimer. Signaling pathways are orchestrated by post-translational modifications (PTMs) such as phosphorylation. Application of PTM-SEA to . Molecular & Cellular Proteomics 18 (3), 576-593 , 2019 [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 Mol Cell Proteomics. 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. Mol Cell Proteom. 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. He has been leading the IOB's efforts in the development and analysis of signaling pathways available through NetPath, a resource of signaling pathways. Author summary Genomic DNA alteration signatures are recurring genomic patterns that are the imprints of mutagenic processes accumulated over the lifetime of cancer cell. 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 .