ComiRNet - The Database of Predicted miRNA Regulatory Networks (Banca dati)

Type
Label
  • ComiRNet - The Database of Predicted miRNA Regulatory Networks (Banca dati) (literal)
Anno
  • 2014-01-01T00:00:00+01:00 (literal)
Alternative label
  • Gianvito Pio (1), Michelangelo Ceci (1), Donato Malerba (1), Domenica D'Elia (2) (2014)
    ComiRNet - The Database of Predicted miRNA Regulatory Networks
    (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#autori
  • Gianvito Pio (1), Michelangelo Ceci (1), Donato Malerba (1), Domenica D'Elia (2) (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#altreInformazioni
  • All target predictions are scored by a learning algorithm that learns to combine the score returned by several prediction algorithms (i.e., 10 stablished miRNA targets prediction programs) by exploiting information conveyed by both labeled (validated interactions, from miRTarBase) and unlabeled (predicted interactions, from mirDIP) instances [1]. MicroRNA regulatory networks are discovered by analyzing scored miRNAs target interactions with the algorithm HOCCLUS2 [2] which: - extracts highly cohesive biclusters, to consider only reliable interactions; - extracts possibly overlapping biclusters, to catch multiple roles of both miRNAs and their target genes; - identifies a hierarchical organization of biclusters, to facilitate bicluster browsing and the identification of \"multiple and cooperative\" miRNA co-targeting on specific groups of genes; - ranks biclusters according to target gene functional similarities to facilitate the retrieval of most significant biclusters. Query & Retrieval ComiRNet database consists of two main modules, each one equipped with a web query interface for the retrieval and visualization of data. A series of filters can be used to refine the query on the basis of different criteria and parameters. The Search Interaction module allows the extraction of miRNA-target predicted interactions on the 3' -UTR of all known Human genes. Results are presented with the score (i.e. probability) assigned by the ComiRNet learning algorithm. The Search Bicluster module hosts predicted interaction networks, identified by HOCCLUS2 from the set of predicted interactions. Associated information are: - bicluster hierarchy level; - involved miRNAs and target genes; - compactness value; - p-values computed on the basis of the intra- and inter- functional similarity of miRNA target-genes. Hierarchy browser provides easy navigation among parents and children biclusters across the hierarchy. Results can be extracted in different formats. Visualization In addition, the system provides a graph-based visualization of interaction networks, which summarizes the predicted associations for a particular bicluster. Nodes represent genes and interacting miRNAs. Edges represent the predicted functional associations. Hovering over an edge will display ComiRNet predicted interaction scores. Network view can be changed by filtering interactions according to the score. References 1. G. Pio, M. Ceci, D. D'Elia, D. Malerba, Integrating microRNA target predictions for the discovery of gene regulatory networks: a semi-supervised ensemble learning approach. BMC Bioinformatics 15 (Suppl 1), S4, 2014 2. G. Pio, M. Ceci, D. D'Elia, C. Loglisci, D. Malerba, A novel biclustering algorithm for the discovery of meaningful biological correlations between miRNAs and mRNAs BMC Bioinformatics 14 (Suppl 7), S8, 2013 (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#url
  • http://193.204.187.158:9002/ (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#supporto
  • Altro (literal)
Http://www.cnr.it/ontology/cnr/pubblicazioni.owl#affiliazioni
  • (1) Department of Computer Science, University of Bari Aldo Moro, Via Orabona 4, 70125, Bari, Italy (2) CNR, Institute for Biomedical Technologies, Via Amendola 122/D, 70126, Bari, Italy (literal)
Titolo
  • ComiRNet - The Database of Predicted miRNA Regulatory Networks (literal)
Descrizione sintetica
  • ComiRNet is a database of miRNA target predictions and predicted miRNA regulatory networks. The database stores approximately 5 million predicted interactions between 934 human miRNAs and 30,875 gene transcripts (mRNAs) which are exploited in the construction of the hierarchies of overlapping biclusters representing potential miRNA regulatory networks. (literal)
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