Tools

04.21.16 by

New network analysis tools on the Genboree Workbench

Sample output from Target Interaction Finder

Sample output from Target Interaction Finder

We recently developed two tools for the Genboree Workbench: Target Interaction Finder and Pathway Finder. Given a set of miRNAs, these tools find miRNA-target interactions and pathway targets from public databases. To support consortium scientists in using these tools, we have created two training videos which describe the necessary input file, how to use the tool, and downstream network visualization in Cytoscape for Target Interaction Finder and Pathway Finder. The videos are available in the collection of ERC consortium videos at YouTube and in the Resources/Presentations section of this website.

The tools are open to anyone with a (free) Genboree account and can be used with any arbitrary input list of miRNA identifiers or with public datasets available in the exRNA Atlas. Target Interaction Finder generates a network of miRNA and protein target interactions, which is returned as a tabular summary and an XGMML formatted network file. The network file can be imported into network visualization and analysis tools like Cytoscape. Pathway Finder generates a table of pathways containing the miRNA and/or their protein targets based on information from WikiPathways. Embedded in the results window of Pathway Finder is an interactive pathway viewer.

Sample Pathway Finder results file

Sample Pathway Finder results file

exRNA_WP_blog_tools-PF-interactive

Interactive Pathway Finder viewer on Genboree Workbench

12.15.15 by

miRandola database: the future of non-invasive diagnosis through circulating RNA biomarkers

Non-coding RNAs (ncRNAs), for example microRNAs (miRNAs), are frequently dysregulated in cancer and other diseases, and have shown great potential as tissue-based markers for cancer classification and prognostication. ncRNAs are present in membrane-bound vesicles, such as exosomes, in extracellular human body fluids. Circulating miRNAs are also present in human plasma and serum and cofractionate with the Argonaute2 (Ago2) protein and high-density lipoprotein (HDL). Since miRNAs and other ncRNAs circulate in the bloodstream in highly stable forms, they may be used as blood-based biomarkers for cancer and other diseases. A knowledge base of non-invasive biomarkers is a fundamental tool for biomedical research in this field.

In 2012, miRandola was developed as the first database of circulating extracellular miRNAs (Russo et al., 2012). miRandola is a comprehensive, manually curated collection and classification of circulating extracellular miRNAs. We recently updated miRandola with 271 papers, 2695 entries, 673 miRNAs and 12 long non-coding RNAs. The future direction of the database is to be a resource for all potential non-invasive circulating nucleic acid biomarkers.

miRandola_schema

miRandola is the first online resource which gathers all the available data on circulating RNAs into one environment (see Figure). It represents a useful reference tool for anyone investigating the role of extracellular RNAs as biomarkers, as well as their physiological function and their involvement in pathologies.

The database is constantly updated as soon as new data is available, and the online submission system is a crucial feature which helps to ensure that the system is always up-to-date. We are working on a second version of the database to increase the amount of data and to improve usability. miRandola is available online at https://mirandola.iit.cnr.it/.

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