With unprecedented increase in next generation sequencing (NGS) technologies, there has been a persistent interest on transcript profiles of long noncoding RNAs (lncRNAs) and protein-coding genes forming an interaction network. Apart from protein-protein interaction (PPI), gene interaction models such as Weighted Gene Co-expression Network Analysis are used to functionally annotate lncRNAs in identifying their potential disease associations. To address this, studies have led to characterizing transcript structures and understanding expression profiles mediating regulatory roles. In the current analysis, we show how a lncRNA- cyp2c91 contributes to the transcriptional regulation localized to cytoplasm thereby making refractory environment for transcription.  By applying co-expression network methods and pathway analyses on genes related to a disease such as obesity from F2 pig model, we show that we can gain deeper insight in biological processes such as the perturbances in immune system and metabolic syndrome, and get a better understanding of the systems biology of diseases.We believe this study has implications for finding prognostic and diagnostic markers for obesity and immune related diseases.