Co-expression tools for plant biology: opportunities for hypothesis generation and caveats

Gene co‐expression analysis has emerged in the past 5 years as a powerful tool for gene function prediction. In essence, co‐expression analysis asks the question ‘what are the genes that are co‐expressed, that is, those that show similar expression profiles across many experiments, with my gene of interest?’. Genes that are highly co‐expressed may be involved in the biological process or processes of the query gene. This review describes the tools that are available for performing such analyses, how each of these perform, and also discusses statistical issues including how normalization of gene expression data can influence co‐expression results, calculation of co‐expression scores and P values, and the influence of data sets used for co‐expression analysis. Finally, examples from the literature will be presented, wherein co‐expression has been used to corroborate and discover various aspects of plant biology.     

Effects of caffeine on germination and differentiation in spores of the fern, Onoclea sensibilis

During spore germination in the fern, Onoclea sensibilis L., the nucleus moves from a central position to one end, and an asymmetrical cell division partitions the spore into two cells of greatly unequal size. The smaller cell differentiates directly into a rhizoid, whereas the larger cell and its derivatives give rise to the prothallus. In the presence of 5 mM caffeine, the nuclei of most of the spores undergo mitotic replication, whereas cell wall formation is blocked. Multinucleate single cells are produced, which are capable of growth, but no rhizoid differentiation occurs. In some cases a partial cell wall is produced, but the nucleus moves through the discontinuity back to the center of the spore, and the enucleate, incompletely partitioned small “cell” fails to differentiate into a rhizoid. In less than 1% of the spores a broad protuberance, whose wall is yellow-brown, is formed in a multinucleate single cell. The color, staining reaction to ruthenium red, and ultrastructural appearance of the protuberance resemble that of the rhizoid wall. It appears that infrequently in the caffeine-treated spores, a feature which is characteristic of rhizoids is expressed, in the absence of asymmetric cell division, in a cell which otherwise is unable to produce a rhizoid. The results are interpreted to mean that the spore has a highly localized, persistent differentiated region. For rhizoid differentiation to occur, a nucleus must be confined in that region – a confinement which normally is accomplished by the geometrically asymmetric first cell division of germination.     

The Effects of Centrifugation on Asymmetric Cell Division and Differentiation of Fern Spores

We have investigated the effects of centrifugation on sporepolarity, asymmetric cell division, and rhizoid differentiationin the sensitive fern Onoclea sensibilis L. Centrifugation at10000 g for 30 min produces a random orientation of spores withstratification of the cell contents. After centrifugation atmost early stages of development, the nucleus retains its normalpattern of migration from the centre of the ellipsoidal sporeto the proximal face and then to an end of the spore, withoutregard to the orientation of stratification. This indicatesthat the polarity of the spore is stable to centrifugation.As long as the nucleus migrates to an end of the spore and asymmetriccell division occurs, the small cell differentiates into a rhizoid.The arrangement of large cytoplasmic organelles appears to haveno influence on nuclear migration, asymmetric cell division,or rhizoid differentiation. The only period during developmentwhen centrifugation blocks asymmetric cell division is immediatelypreceding and during mitosis and cytokinesis. Spores centrifugedat this stage do not complete nuclear migration, and symmetriccell division results, with neither cell differentiating intoa rhizoid. The source of the stable polarity of the spore isdiscussed. cell polarity, rhizoid differentiation, centrifugation, Onoclea sensibilis L., sensitive fern, fern spores