Functional annotation and network reconstruction through cross-platform integration of microarray data

Xianghong Jasmine Zhou, Ming Chih J. Kao, Haiyan Huang, Angela Wong, Juan Nunez-Iglesias, Michael Primig, Oscar M. Aparicio, Caleb E. Finch, Todd E. Morgan, Hung Wong Wing

Research output: Contribution to journalArticleResearchpeer-review

122 Citations (Scopus)


The rapid accumulation of microarray data translates into a need for methods to effectively integrate data generated with different platforms. Here we introduce an approach, 2nd-order expression analysis, that addresses this challenge by first extracting expression patterns as meta-information from each data set (1st-order expression analysis) and then analyzing them across multiple data sets. Using yeast as a model system, we demonstrate two distinct advantages of our approach: we can identify genes of the same function yet without coexpression patterns and we can elucidate the cooperativities between transcription factors for regulatory network reconstruction by overcoming a key obstacle, namely the quantification of activities of transcription factors. Experiments reported in the literature and performed in our lab support a significant number of our predictions.

Original languageEnglish
Pages (from-to)238-243
Number of pages6
JournalNature Biotechnology
Issue number2
Publication statusPublished - 1 Feb 2005
Externally publishedYes

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