Abstract
Although long noncoding RNAs (lncRNAs) have been recognized in recent years to constitute a significant portion of mammalian transcriptome, and the functional impact of several lncRNAs has been characterized by a few studies, yet it is still difficult to large-scale ascertain their functions from lab experiment or structure prediction. To address this deficit, we have developed a computational pipeline to large-scale annotate the functions of lncRNA based on coding–noncoding gene co-expression network. In this network, a node (circle) represents the protein-coding gene or lncRNA, and an edge (connecting line between nodes) indicates that the two genes are co-expressed (the correlation coefficients of connected genes reached the defined cutoff). In this chapter, we show how to use an lncRNA functional annotation pipeline to construct a co-expression network based on gene expression profiles in prostate cancer and how to further predict lncRNA functions using model-based and hub-based sub-networks.
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References
Liao Q, Liu C, Yuan X et al (2011) Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network. Nucleic Acids Res 39:3864–3878
Bu D, Yu K, Sun S et al (2012) NONCODE v3.0: integrative annotation of long noncoding RNAs. Nucleic Acids Res 40:D210–D215
Mercer TR, Dinger ME, Mattick JS (2009) Long non-coding RNAs: insights into functions. Nat Rev Genet 10:155–159
Pandey RR, Mondal T, Mohammad F et al (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232–246
Zhao Y, He S, Liu C et al (2008) MicroRNA regulation of messenger-like noncoding RNAs: a network of mutual microRNA control. Trends Genet 24:323–327
Huarte M, Guttman M, Feldser D et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409–419
Liao Q, Xiao H, Bu D et al (2011) ncFANs: a web server for functional annotation of long non-coding RNAs. Nucleic Acids Res 39:W118–W124
Guo X, Gao L, Liao Q et al (2013) Long non-coding RNAs function annotation: a global prediction method based on bi-colored networks. Nucleic Acids Res 41:e35
Flicek P, Amode MR, Barrell D et al (2012) Ensembl 2012. Nucleic Acids Res 40:D84–D90
Cabili MN, Trapnell C, Goff L et al (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915–1927
Derrien T, Johnson R, Bussotti G et al (2012) The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. Genome Res 22:1775–1789
Ashurst JL, Chen CK, Gilbert JG et al (2005) The Vertebrate Genome Annotation (Vega) database. Nucleic Acids Res 33:D459–D465
Trapnell C, Williams BA, Pertea G et al (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol 28:511–515
Ashburner M, Ball CA, Blake JA et al (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25:25–29
Dechat T, Vlcek S, Foisner R (2000) Review: lamina-associated polypeptide 2 isoforms and related proteins in cell cycle-dependent nuclear structure dynamics. J Struct Biol 129:335–345
Borodovsky M, Peresetsky A (1994) Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy. Comput Chem 18:259–267
Merico D, Isserlin R, Stueker O et al (2010) Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS One 5:e13984
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Zhao, Y., Luo, H., Chen, X., Xiao, Y., Chen, R. (2014). Computational Methods to Predict Long Noncoding RNA Functions Based on Co-expression Network. In: Alvarez, M., Nourbakhsh, M. (eds) RNA Mapping. Methods in Molecular Biology, vol 1182. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-1062-5_19
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DOI: https://doi.org/10.1007/978-1-4939-1062-5_19
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