PMC:4996411 / 36337-38018 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/4996411","sourcedb":"PMC","sourceid":"4996411","source_url":"https://www.ncbi.nlm.nih.gov/pmc/4996411","text":"4.1. Data Handling\nAn important, but often underestimated, task of RPPA data analysis is sample management and sample tracking. Most existing solutions of RPPA data analysis tools neglect this aspect. The “SuperCurve” suite provides a tcl/tk-based graphical user interface, which eases the data management for experimental biologists. The other tools expect either basic knowledge with R, are not sufficiently documented or were only implemented as post-analysis tools. Only MIRACLE (Table 1) enables a biologist-friendly web-interface that is easily accessible and supports R with a direct import/export interface for data analysts with experience in programming [30].\nThe complexity of RPPA data also suggests implementing a data management system for standardization of RPPA data. Such a concept was introduced by Stanislaus et al. [39] who tried to form an RPPA Information Management System in 2008, including a reverse phase protein array markup language (RPPAML) to describe, document and disseminate RPPA data. Currently, the project is apparently not further maintained although it would be beneficial for the growing RPPA community. Reasons for this could be the implementation of RPPAML for the commercial software MATLAB while not providing an interface to R methods that are widely used in this field. MIRACLE [30] can currently substitute some of the data handling and sample tracking functionalities needed as it balances user-friendliness and flexibility. However, standardized RPPA data analysis programs are required to handle the complex information associated with proteomic experimentation and to make this information available for public proteomic databases.","divisions":[{"label":"Title","span":{"begin":0,"end":18}}],"tracks":[{"project":"2_test","denotations":[{"id":"27600238-25161257-69479250","span":{"begin":665,"end":667},"obj":"25161257"},{"id":"27600238-19102773-69479251","span":{"begin":836,"end":838},"obj":"19102773"},{"id":"27600238-25161257-69479252","span":{"begin":1324,"end":1326},"obj":"25161257"}],"attributes":[{"subj":"27600238-25161257-69479250","pred":"source","obj":"2_test"},{"subj":"27600238-19102773-69479251","pred":"source","obj":"2_test"},{"subj":"27600238-25161257-69479252","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#e793ec","default":true}]}]}}