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InCroMAP: Integrated analysis of Cross-platform MicroArray and Pathway data.
MedLine Citation:
PMID:  23257199     Owner:  NLM     Status:  Publisher    
Abstract/OtherAbstract:
SUMMARY: 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 very small, compared to mRNA analysis tools. Especially, a joint analysis of different microarray platforms that have been employed on the same set of biological samples is hardly supported by most microarray analysis tools.We here 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 signaling pathways. AVAILABILITY: 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. CONTACT: clemens.wrzodek@uni-tuebingen.de.
Authors:
Clemens Wrzodek; Johannes Eichner; Finja Büchel; Andreas Zell
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Publication Detail:
Type:  JOURNAL ARTICLE     Date:  2012-12-20
Journal Detail:
Title:  Bioinformatics (Oxford, England)     Volume:  -     ISSN:  1367-4811     ISO Abbreviation:  Bioinformatics     Publication Date:  2012 Dec 
Date Detail:
Created Date:  2012-12-21     Completed Date:  -     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  9808944     Medline TA:  Bioinformatics     Country:  -    
Other Details:
Languages:  ENG     Pagination:  -     Citation Subset:  -    
Affiliation:
Center for Bioinformatics Tuebingen (ZBIT), University of Tuebingen, 72076 Tübingen, Germany.
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