High-throughput sequencing technologies, in particular RNA sequencing (RNA-seq), have become the basic practice for genomic studies in biomedical research. In addition to studying genes individually, for example, through differential expression analysis, investigating co-ordinated expression variations of genes may help reveal the underlying cellular mechanisms to derive better understanding and more effective prognosis and intervention strategies. Although there exists a variety of co-expression network based methods to analyze microarray data for this purpose, instead of blindly extending these methods for microarray data that may introduce unnecessary bias, it is crucial to develop methods well adapted to RNA-seq data to identify the functional modules of genes with similar expression patterns.