Abstract:
BACKGROUND:Identifying the interactions between proteins and long non-coding RNAs (lncRNAs) is of great importance to decipher the functional mechanisms of lncRNAs. However, current experimental techniques for detection of lncRNA-protein interactions are limited and inefficient. Many methods have been proposed to predict protein-lncRNA interactions, but few studies make use of the topological information of heterogenous biological networks associated with the lncRNAs. RESULTS:In this work, we propose a novel approach, PLIPCOM, using two groups of network features to detect protein-lncRNA interactions. In particular, diffusion features and HeteSim features are extracted from protein-lncRNA heterogenous network, and then combined to build the prediction model using the Gradient Tree Boosting (GTB) algorithm. Our study highlights that the topological features of the heterogeneous network are crucial for predicting protein-lncRNA interactions. The cross-validation experiments on the benchmark dataset show that PLIPCOM method substantially outperformed previous state-of-the-art approaches in predicting protein-lncRNA interactions. We also prove the robustness of the proposed method on three unbalanced data sets. Moreover, our case studies demonstrate that our method is effective and reliable in predicting the interactions between lncRNAs and proteins. AVAILABILITY:The source code and supporting files are publicly available at: http://denglab.org/PLIPCOM/ .
journal_name
BMC Bioinformaticsjournal_title
BMC bioinformaticsauthors
Deng L,Wang J,Xiao Y,Wang Z,Liu Hdoi
10.1186/s12859-018-2390-0subject
Has Abstractpub_date
2018-10-11 00:00:00pages
370issue
1issn
1471-2105pii
10.1186/s12859-018-2390-0journal_volume
19pub_type
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