NetMiner – an ensemble pipeline for building genome-wide and high-quality gene co-expression network using massive-scale RNA-seq samples

Accurately reconstructing gene co-expression network is of great importance for uncovering the genetic architecture underlying complex and various phenotypes. The recent availability of high-throughput RNA-seq sequencing has made genome-wide detecting and quantifying of the novel, rare and low-abundance transcripts practical. However, its potential merits in reconstructing gene co-expression network have still not been well explored. Using massive-scale RNA-seq samples, researchers at Nantong University have designed an ensemble pipeline, called NetMiner, for building genome-scale and high-quality Gene Co-expression Network (GCN) by integrating three frequently used inference algorithms. The researchers constructed a RNA-seq-based GCN in one species of monocot rice. The quality of network obtained by this method was verified and evaluated by the curated gene functional association data sets, which obviously outperformed each single method. In addition, the powerful capability of network for associating genes with functions and agronomic traits was shown by enrichment analysis and case studies. In particular, they demonstrated the potential value of the proposed method to predict the biological roles of unknown protein-coding genes, long non-coding RNA (lncRNA) genes and circular RNA (circRNA) genes. These results provided a valuable and highly reliable data source to select key candidate genes for subsequent experimental validation. To facilitate identification of novel genes regulating important biological processes and phenotypes in other plants or animals, the researchers have published the source code of NetMiner.

Flowchart of high-quality RNA-seq-based gene co-expression network inference

Availability – NetMiner is freely available at https://github.com/czllab/NetMiner.