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

welcoming the future by Brandon Hoover via Flickr

Nature Biotechnology:

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, 2(nd)-order expression analysis, that addresses this challenge by first extracting expression patterns as meta-information from each data set (1(st)-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.


Technorati Tags:
Publications / Computational biolgy / statistics / Gene expression analysis / 2nd-order analysis / Wing Hung Wong / Xianghong Jasmine Zhou / Haiyan Huang