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Functional annotation and network reconstruction through cross-platform integration of microarray data
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Functional annotation and network reconstruction through cross-platform integration of microarray data
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Journal Article
Functional annotation and network reconstruction through cross-platform integration of microarray data
2005
Overview
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.
Publisher
Nature Publishing Group US,Nature,Nature Publishing Group
Subject
/ Biological and medical sciences
/ Biomedical and Life Sciences
/ Biomedical Engineering/Biotechnology
/ Fundamental and applied biological sciences. Psychology
/ Fungal Proteins - metabolism
/ Gene Expression Profiling - methods
/ Gene Expression Regulation, Fungal - physiology
/ letter
/ Molecular and cellular biology
/ Oligonucleotide Array Sequence Analysis - methods
/ Signal Transduction - physiology
/ Transcription Factors - genetics
/ Transcription Factors - metabolism
/ Yeasts
