EMBnet.journal

LP-HCLUS: a novel tool for the prediction of relationships between ncRNAs and human diseases

Emanuele Pio Barracchia1,2✉, Gianvito Pio1,2, Domenica D’Elia3, Michelangelo Ceci1,2,4

1 Department of Computer Science, University of Bari Aldo Moro, Bari, Italy

2 National Interuniversity Consortium for Informatics (CINI), Rome, Italy

3 Institute for Biomedical Technologies, National Research Council, Bari, Italy

4 Department of Knowledge Technologies, Jozef Stefan Institute, Ljubljana, Slovenia

Competing interests: EPB none; GP none; DD none; MC none

 

The discovery of a functional relationship between human diseases and non-coding RNAs (ncRNAs) is not new. In the last decade, it improved the elucidation of many diseases’ mechanisms and the improvement of therapeutic approaches (Lekka and Hall, 2018; Wang et al., 2016; Yang et al., 2014). Nevertheless, the function of many ncRNAs is still unclear or completely unknown, and therefore, their role in human diseases is difficult, if not impossible, to be identified. We have developed a new system, called LP-HCLUS, that is able to predict previously unknown disease-ncRNA associations by exploiting multi-type hierarchical clustering techniques.

Differently from other approaches, LP-HCLUS is able to analyse and benefit from heterogeneous networks of interactions/relationships among multiple types of entities (e.g., diseases, ncRNAs, target genes) and relationships between them. To this aim, the proposed method first estimates the strength of the disease-ncRNA associations, exploiting both direct and indirect relationships. It constructs a hierarchy of heterogeneous clusters based on known and estimated relationships between diseases and ncRNAs. Finally, LP-HCLUS uses the generated clusters to induce new relationships, associating each of them with a certainty score. We conducted several experiments, comparing the performances achieved by LP-HCLUS with those obtained by two different competitors: HOCCLUS2 (Pio et al., 2013) and ncPred (Alaimo et al., 2014). In particular, we analysed two different datasets: HMDD v3.0, which contains data about relationships between diseases and miRNAs, and a dataset constructed integrating different state-of-the-art data sources (Chen et al., 2013; Helwak et al., 2013; Bauer-Mehren et al., 2010; Jiang et al., 2009).

The results show that our system is able to outperform its competitors, and it can help biologists to conduct more focused research. Such a conclusion is also confirmed by a qualitative analysis conducted on the predicted associations that showed that many associations predicted by LP-HCLUS with a high certainty score have been subsequently validated and introduced in a more recent version of HMDD dataset (v3.2). The importance of such a development is also in its easy transfer for applications in any biological study involving heterogeneous data from different sources and types (e.g., different omics data, chemicals, biochemical and structural data, etc.).

 

Availability of data and materials

The system LP-HCLUS, the adopted datasets and all the results are available at: http://www.di.uniba.it/~gianvitopio/systems/lphclus/

Acknowledgements

We would like to acknowledge the financial support of the European Commission through the project MAESTRA - Learning from Massive, Incompletely annotated, and Structured Data (Grant Number ICT-2013-612944). We also acknowledge the financial support of the Ministry of Education, Universities and Research (MIUR) through the PON projects “Big Data Analytics” (AIM1852414 - Activity 1, Line 1) and TALIsMAn - Tecnologie di Assistenza personALizzata per il Miglioramento della quAlità della vitA (Grant N. ARS01_0111), and of Italian National Research Council (CNR) through the InterOmics Flagship project.

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