Conclusion

  Given that many proteins carry out their biological functions by the integrated activities of interacting proteins, the aim of this paper was to establish whether the list of proteins previously identified by 2DE proteomics analysis  in the work by Ingle et al. (2007) could perform biological interactions.   Network analysis can not only predict possible interactions between the proteins in the query list but can also predict associated proteins that act together with the proteins in the query list. The additional protein/gene list can be useful for future biotechnological applications. Results from this work show that proteins in each set (de novo, up-regulated and down-regulated) are mostly connected. PPI analysis identified many other proteins/genes that connect the query proteins together. This has provided a longer list of proteins/genes for each set. Before these added proteins can be of much interest, the differential expression patterns of the predicted associated proteins need wet lab validation.  Further, functional enrichment analysis identified statistically significant GO biological process terms that are associated with each set. The approach used in this work is capable of generating novel inferences from resurrection plants proteomics data that has already been published thereby providing more information from data that is yet to be fully exploited.

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