Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

By Q. Liao, Changning Liu, Xiongying Yuan, Shuli Kang, Ruoyu Miao, Hui Xiao, Guoguang Zhao, Haitao Luo, Dechao Bu, Haitao Zhao and 3 more. Nucleic Acids Research, 2011

526 citations recorded by the source corpus.

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).

Subfields: Cancer Research, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5de02b8afab25648152523a1a66c544dc135c6f8

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In Molecular Biology

1. Michael Q. Zhang
2. Yi Zhao
3. Runsheng Chen
4. Wei Wu
5. Xiaoxi Zeng

Citations in the corpus

• HERB: a high-throughput experiment- and reference-guided database of traditional Chinese medicine (2020, background): “With more and diverse data becoming available, further studies based on these data will be required for analyzing the gene regulation networks under the herb/ingredient perturbation (51,52), and identifying new types of diseaserelevant genes (53,54).”
• NONCODE v3.0: integrative annotation of long noncoding RNAs (2011, methodology): “0 now also includes expressional and functional lncRNA data (13,14) obtained from re-annotated microarray studies.”
• NONCODE 2016: an informative and valuable data source of long non-coding RNAs (2015, methodology): “Functions for the lncRNA genes were predicted by lnc-GFP (25), a coding–non-coding co-expression network (26,27) based global function predictor.”
• NONCODEv4: exploring the world of long non-coding RNA genes (2013, methodology): “Each transcript in NONCODE is annotated with the following information:(i) basic description, including the ncRNA name, alias, sequence, length, genomic location, coding potential assessment by CPC (27) and CNCI, organisms and references; (ii) biological information, concerning its function, cellula”
• Long noncoding RNA high expression in hepatocellular carcinoma facilitates tumor growth through enhancer of zeste homolog 2 in humans (2011, methodology): “We used gene coexpression networks to cluster thousands of transcripts into phenotypically relevant coexpression modules.(17,21) The structure of the coexpression networks of HCC and nontumor samples were significantly different (Supporting Figs.”