Comparative network analysis of gene co-expression networks reveals the conserved and species-specific functions of cell-wall related genes between Arabidopsis and Poplar

In this study, we established a computational framework of comparative network analysis to identify the conserved and species-specific functions of cell-wall (CW) related genes [1, 2], an important gene family related to plant bio-fuel productions across multiple tissue types between Arabidopsis and Poplar. The co-expressed genes are believed to coordinate in transcription so that they may have similar functions [3, 4]. Also, a comparative analysis across species for gene co-expression networks (GCNs) provides a systematic way to understand genomic conserved or species-specific functions [5]. Therefore, to understand the functions of CW genes in different tissue types, we integrated and compared the network characteristics of CW genes across GCNs from different tissue types including leaf, flower and shoot for Arabidopsis and Poplar [6]. First, by aligning the gene co-expression sub-networks associated with CW genes between two plants for each tissue type, we grouped the tissue types based on the alignment of the CW genes along with their neighboring orthologous genes. For those tissues with good alignments, it suggests that CW genes coordinate in a similar way for both plants, which may have involved in the conserved functions. For the tissues with poor alignments, however, CW genes may take part in species-specific functions. The gene ontology enrichment and signaling pathways of their co-expressed neighboring genes were identified to provide new insight for cell wall biology. Second, since the genes with high network centralities of a GCN, so called "hub" genes, are believed to have key functions [7], we investigated the network centralities for the CW genes between two plants to understand their functions in a global network point of view. The network centralities of GCN that we used are clustering coefficient (CC) for measuring gene's local cliqueness, and eigenvector centrality (EC) for measuring gene's global influence over the entire network. Besides finding hub genes for each tissue type within and across two plants, we also identified the conserved hub genes and tissue-specific hub genes in either local or global fashion. The CW genes that happen to become hub were particularly of interest to study. If many CW genes are global hubs in certain tissues, it implies that cell wall related activities may interact with the whole plant in those tissues, but if local hubs, they may coordinate with certain local activities only. Finally, we used the genomic variation data to identify the species-specific SNPs, especially in the promoter regions of the CW co-expressed neighboring genes across tissues, and associate them with corresponding species-specific functions. In summary, our comparative network analysis framework studied gene co-expression networks for the cell wall related genes across different tissue types in Arabidopsis and Poplar, and identified their conserved and species-specific functions and variations. This framework can also be used to study other gene families along with their functions across multiple species.