title: InCroMAP: integrated analysis of cross-platform microarray and pathway data.
abstract: CONCLUSIONS
  Microarrays are commonly used to detect changes in gene expression between different biological samples. For this purpose, many analysis tools have been developed that offer visualization, statistical analysis and more sophisticated analysis methods. Most of these tools are designed specifically for messenger RNA microarrays. However, today, more and more different microarray platforms are available. Changes in DNA methylation, microRNA expression or even protein phosphorylation states can be detected with specialized arrays. For these microarray technologies, the number of available tools is small compared with mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been used on the same set of biological samples is hardly supported by most microarray analysis tools. Here, we present InCroMAP, a tool for the analysis and visualization of high-level microarray data from individual or multiple different platforms. Currently, InCroMAP supports mRNA, microRNA, DNA methylation and protein modification datasets. Several methods are offered that allow for an integrated analysis of data from those platforms. The available features of InCroMAP range from visualization of DNA methylation data over annotation of microRNA targets and integrated gene set enrichment analysis to a joint visualization of data from all platforms in the context of metabolic or signalling pathways.
  
  
  BACKGROUND
  InCroMAP is freely available as Java™ application at www.cogsys.cs.uni-tuebingen.de/software/InCroMAP, including a comprehensive user's guide and example files.
authors.affiliation: Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany. clemens.wrzodek@uni-tuebingen.de
authors.forename: Clemens
authors.initials: C
authors.lastname: Wrzodek
authors.forename: Johannes
authors.initials: J
authors.lastname: Eichner
authors.forename: Finja
authors.initials: F
authors.lastname: Büchel
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
mesh_terms: D019175:DNA Methylation; D015870:Gene Expression; D020869:Gene Expression Profiling; D035683:MicroRNAs / Q000378:metabolism; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D040081:Protein Array Analysis; D011506:Proteins / Q000378:metabolism; D012333:RNA, Messenger / Q000378:metabolism; D012984:Software
chemical_list: D035683:MicroRNAs; D011506:Proteins; D012333:RNA, Messenger