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Microarray Data Analysis Tools

  • BRB Tools
BRB ArrayTools is a powerful microarray data analysis package. Both supervised and unsupervised analysis are supported, such as permutation t-test or F-test, cluster analysis, principal component analysis, and so on. Users can perform data cleaning, normalization, class comparison, class prediction, survival test, and other statistical analysis on their data based on specific experiment design. Annotations can also be retrieved from NCI or Affymetrix if available. It works as an Excel adds-in and is very easy to use.

  • ICBR AnalyzeIt Tools
AnalyzeIt is designed and developed at ICBR and works as one of the major analysis tools in our researches. Based on different experiment design, 1-way, 2-way or 3-way ANOVA analysis followed by TukeyHSD test can be applied in a batch mode. The result is written into an Excel file for further processing. Probes from Affymetrix chips can be annotated in a second and used to generate a Gene Ontology tree showing the functional relationships among differentially expressed genes. AnalyzeIt also has some utility tools, such as set operations and data preparation for GenMAPP pathway, to facilitate customized data analysis.

  • Cluster & TreeView
Cluster performs cluster analysis using various algorithms, including Hierachical Clustering, K-Means Clustering, Self Organizing Maps, and PCA. Some simple data cleaning, transformation and normalization are also supported. The resulted clusters can be viewed using TreeView.

  • Pathway & Function Analysis
Pathway and function analysis is an unbreakable part for microarray data analysis. GenMAPP and KEGG pathway information and Gene Ontology terms are included in many probe annotations. Linking gene expression data to those pathway and function information will reveal very important expression and regulation patterns.
GenMAPP provides a program that can apply user-defined color schema to its pathway mapps, based on gene expression data. An utility tool that helps users to prepare the data set ready for GenAMPP from Affymetrix chips are integrated into ICBR AnalyzeIt software.
Gene Ontology is a set of controlled vocabulary used to classifying molecular function, cellular component, and biological process. Terms in Gene Ontology is maintained in a hierachical structure, which we call "gene ontology tree". AnalyzeIt software allows users to populate this gene ontology tree with their expression data to investigate if there are some observable functional groups or regulation patterns.