The deregulation of non-coding RNAs (ncRNAs) has a functional role in cancer and other human disorders [1, 2]. Reconstructing and visualizing networks of ncRNAs interactions with diseases and candidate targeting genes is important to understand their regulatory mechanism in complex cellular systems. Within ncRNA-DB [3], we have recently imported and integrated associations among non-coding RNAs, protein coding genes, and associated diseases from ten on-line databases. Up to date it contains about 300 thousands associations. To improve the usability of such a complex integrated system, it has to be equipped with a methodology leading users to weight the connections linking the ncRNAs to genes and to diseases. We elaborate a scoring methodology based on literature mining, network analysis, and alignment-free sequence algorithms, to rank the ncRNA-disease and ncRNA-gene associations reported in ncRNA-DB. The Lit-Score takes into account the frequencies of co-occurrence in PubMed and in ncRNA-DB of the pairs ncRNA-gene, ncRNA-disease, and gene-disease.
A scoring methodology for an integrated network of non-coding RNAs and genetic diseases
Bonnici, Vincenzo;FRANCO, Giuditta;BOMBIERI, Nicola;GIUGNO, ROSALBA
2015-01-01
Abstract
The deregulation of non-coding RNAs (ncRNAs) has a functional role in cancer and other human disorders [1, 2]. Reconstructing and visualizing networks of ncRNAs interactions with diseases and candidate targeting genes is important to understand their regulatory mechanism in complex cellular systems. Within ncRNA-DB [3], we have recently imported and integrated associations among non-coding RNAs, protein coding genes, and associated diseases from ten on-line databases. Up to date it contains about 300 thousands associations. To improve the usability of such a complex integrated system, it has to be equipped with a methodology leading users to weight the connections linking the ncRNAs to genes and to diseases. We elaborate a scoring methodology based on literature mining, network analysis, and alignment-free sequence algorithms, to rank the ncRNA-disease and ncRNA-gene associations reported in ncRNA-DB. The Lit-Score takes into account the frequencies of co-occurrence in PubMed and in ncRNA-DB of the pairs ncRNA-gene, ncRNA-disease, and gene-disease.
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