title: Functional annotation and network reconstruction through cross-platform integration of microarray data.
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, 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.
authors.forename: Xianghong Jasmine
authors.initials: XJ
authors.lastname: Zhou
authors.forename: Ming-Chih J
authors.initials: MC
authors.lastname: Kao
authors.forename: Haiyan
authors.initials: H
authors.lastname: Huang
authors.forename: Angela
authors.initials: A
authors.lastname: Wong
authors.forename: Juan
authors.initials: J
authors.lastname: Nunez-Iglesias
authors.forename: Michael
authors.initials: M
authors.lastname: Primig
authors.forename: Oscar M
authors.initials: OM
authors.lastname: Aparicio
authors.forename: Caleb E
authors.initials: CE
authors.lastname: Finch
authors.forename: Todd E
authors.initials: TE
authors.lastname: Morgan
authors.forename: Wing Hung
authors.initials: WH
authors.lastname: Wong
mesh_terms: D000465:Algorithms; D003198:Computer Simulation; D005656:Fungal Proteins / Q000235:genetics / Q000378:metabolism*; D020869:Gene Expression Profiling / Q000379:methods*; D015966:Gene Expression Regulation, Fungal / Q000502:physiology*; D008954:Models, Biological; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D015398:Signal Transduction / Q000502:physiology*; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism
chemical_list: D005656:Fungal Proteins; D014157:Transcription Factors