Integrative Array Analyzer: a software package for analysis of cross-platform and cross-species microarray data

The rapid accumulation of microarray data translates into an urgent need for tools to perform integrative microarray analysis. Integrative Array Analyzer is a comprehensive analysis and visualization software toolkit, which aims to facilitate the reuse of the large amount of cross-platform and cross-species microarray data. It is composed of the data preprocess module, the co-expression analysis module, the differential expression analysis module, the functional and transcriptional annotation module and the graph visualization module.

[1]  T. Barrette,et al.  Meta-analysis of microarrays: interstudy validation of gene expression profiles reveals pathway dysregulation in prostate cancer. , 2002, Cancer research.

[2]  Homin K. Lee,et al.  Coexpression analysis of human genes across many microarray data sets. , 2004, Genome research.

[3]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[4]  M. Kanehisa A database for post-genome analysis. , 1997, Trends in genetics : TIG.

[5]  T. Golub,et al.  A Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer , 2003, Cell.

[6]  D. Koller,et al.  A module map showing conditional activity of expression modules in cancer , 2004, Nature Genetics.

[7]  Michael Y. Galperin The Molecular Biology Database Collection: 2005 update , 2004, Nucleic Acids Res..

[8]  Sangsoo Kim,et al.  Combining multiple microarray studies and modeling interstudy variation , 2003, ISMB.

[9]  Jiawei Han,et al.  Mining coherent dense subgraphs across massive biological networks for functional discovery , 2005, ISMB.

[10]  W. Wong,et al.  Functional annotation and network reconstruction through cross-platform integration of microarray data , 2005, Nature Biotechnology.

[11]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[12]  T. Heinemeyer,et al.  Expanding the TRANSFAC database towards an expert system of regulatory molecular mechanisms , 1999, Nucleic Acids Res..