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We use tools from functional data analysis to study dynamic changes by relating temporal gene expression profiles of different developmental stages to each other.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>We demonstrate that functional regression methodology can pinpoint relationships that exist between temporary gene expression profiles for different life cycle phases and incorporates dimension reduction as needed for these high-dimensional data. By applying these tools, gene expression profiles for pupa and adult phases are found to be strongly related to the profiles of the same genes obtained during the embryo phase. Moreover, one can distinguish between gene groups that exhibit relationships with positive and others with negative associations between later life and embryonal expression profiles. Specifically, we find a positive relationship in expression for muscle development related genes, and a negative relationship for strictly maternal genes for<jats:italic>Drosophila<\/jats:italic>, using temporal gene expression profiles.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>Our findings point to specific reactivation patterns of gene expression during the<jats:italic>Drosophila<\/jats:italic>life cycle which differ in characteristic ways between various gene groups. Functional regression emerges as a useful tool for relating gene expression patterns from different developmental stages, and avoids the problems with large numbers of parameters and multiple testing that affect alternative approaches.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1471-2105-9-60","type":"journal-article","created":{"date-parts":[[2009,8,4]],"date-time":"2009-08-04T15:07:57Z","timestamp":1249398477000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Inferring gene expression dynamics via functional regression analysis"],"prefix":"10.1186","volume":"9","author":[{"given":"Hans-Georg","family":"M\u00fcller","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeng-Min","family":"Chiou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xiaoyan","family":"Leng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,1,28]]},"reference":[{"key":"2045_CR1","volume-title":"Developmental Biology","author":"SF Gilbert","year":"2000","unstructured":"Gilbert SF: Developmental Biology. 6th edition. 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