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- Title
Functional annotation and network reconstruction through cross-platform integration of microarray data.
- Authors
Zhou, Xianghong Jasmine; Kao, Ming-Chih J; Huang, Haiyan; Wong, Angela; Nunez-Iglesias, Juan; Primig, Michael; Aparicio, Oscar M; Finch, Caleb E; Morgan, Todd E; Wong, Wing Hung
- Abstract
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.
- Subjects
GENETIC transcription; PROTEINS; TRANSCRIPTION factors; YEAST; LEAVENING agents; ANNOTATIONS
- Publication
Nature Biotechnology, 2005, Vol 23, Issue 2, p238
- ISSN
1087-0156
- Publication type
Article
- DOI
10.1038/nbt1058