Large-scale prediction of long non-coding RNA functions in a coding-non-coding gene co-expression network.
Although accumulating evidence has provided insight into the various functions of long-non-coding RNAs (lncRNAs), the exact functions of the majority of such transcripts are still unknown. Here, we report the first computational annotation of lncRNA functions based on public microarray expression profiles. A coding-non-coding gene co-expression (CNC) network was constructed from re-annotated Affymetrix Mouse Genome Array data. Probable functions for altogether 340 lncRNAs were predicted based on topological or other network characteristics, such as module sharing, association with network hubs and combinations of co-expression and genomic adjacency. The functions annotated to the lncRNAs mainly involve organ or tissue development (e.g. neuron, eye and muscle development), cellular transport (e.g. neuronal transport and sodium ion, acid or lipid transport) or metabolic processes (e.g. involving macromolecules, phosphocreatine and tyrosine).
Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Advanced Computing Research Laboratory, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, PR China.
Qi
Q
Liao
Changning
C
Liu
Xiongying
X
Yuan
Shuli
S
Kang
Ruoyu
R
Miao
Hui
H
Xiao
Guoguang
G
Zhao
Haitao
H
Luo
Dechao
D
Bu
Haitao
H
Zhao
Geir
G
Skogerbø
Zhongdao
Z
Wu
Yi
Y
Zhao
D000818:Animals; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D023281:Genomics; D051379:Mice; D058977:Molecular Sequence Annotation; D015341:Nucleic Acid Probes / Q000737:chemistry; D020411:Oligonucleotide Array Sequence Analysis; D022661:RNA, Untranslated / Q000378:metabolism / Q000502:physiology*; D009435:Synaptic Transmission / Q000235:genetics
D015341:Nucleic Acid Probes; D022661:RNA, Untranslated
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