Computational Systems Biology Methods and Protocols.7z

Chapter 12

Identifying Interactions Between Long Noncoding RNAs

and Diseases Based on Computational Methods

Wei Lan, Liyu Huang, Dehuan Lai, and Qingfeng Chen

Abstract

With the development and improvement of next-generation sequencing technology, a great number of
noncoding RNAs have been discovered. Long noncoding RNAs (lncRNAs) are the biggest kind of
noncoding RNAs with more than 200 nt nucleotides in length. There are increasing evidences showing
that lncRNAs play key roles in many biological processes. Therefore, the mutation and dysregulation of
lncRNAs have close association with a number of complex human diseases. Identifying the most likely
interaction between lncRNAs and diseases becomes a fundamental challenge in human health. A common
view is that lncRNAs with similar function tend to be related to phenotypic similar diseases. In this chapter,
we firstly introduce the concept of lncRNA, their biological features, and available data resources. Further,
the recent computational approaches are explored to identify interactions between long noncoding RNAs
and diseases, including their advantages and disadvantages. The key issues and potential future works of
predicting interactions between long noncoding RNAs and diseases are also discussed.

KeywordsLong noncoding RNA, Human disease, Biological networks, Heterogeneous data fusion,

Machine learning

1 Introduction

With the completion of human genome project, only 2% in human

genome were identified [1–3]. It means that about 98% of human

genome does not encode protein sequences and these genome

regions usually transcribe as noncoding RNA [4–6]. For a long

time, noncoding RNAs (ncRNAs) have been viewed as transcrip-

tional noise in biology [7–10]. However, more and more researches

have shown that noncoding RNAs perform critical roles in many

biological processes [11–14]. There are different kinds of function-

ally important RNAs such as small nucleolar RNA (snoRNA),

microRNA (miRNA), small interfering RNA (siRNA), extracellular

RNA (exRNA), piwi-interacting RNA (piRNA), small Cajal body

RNA (scaRNA), and long noncoding RNA (lncRNA) [15, 16].

Tao Huang (ed.),Computational Systems Biology: Methods and Protocols, Methods in Molecular Biology, vol. 1754,
https://doi.org/10.1007/978-1-4939-7717-8_12,©Springer Science+Business Media, LLC, part of Springer Nature 2018

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