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Microarray and Multimodal Imaging Data Analysis Solutions

Microarray Data Analysis

Microarray experiments are usually designed in the perspective of the analysis strategy.  Alternatively one can devise an analysis strategy to make the best use of available data. Global expression patterns of thousands of genes are initially examined and then a small subset of significant genes is identified.  Functional analysis of these genes and data mining are next steps in understanding the results. There is a learning curve in this process because of the developing nature of this technology. Experience in bioinformatics, statistics, data mining, software and biology counts to achieve best results.  Array technology has limitations and validation of results is warranted.

The routine microarray data analysis can be divided into the following steps:

1. Definition of project: Aim of study, design of project, number of samples, array platform and number of probes, analysis strategy, significance criteria, list of analysis results.
2. Preliminary Analysis: Collation of data,
Checks on the quality of raw data including feature quality check, global expression patterns, summary of number of significant genes, and
Preliminary analysis report.
3. Identification of Genes: Statistical analysis to list out significantly altered genes by class comparisons (one or two sample t-tests) and false discovery estimates or as specified by the definition of project.
Tables of gene lists. Hyperlinks to standard databases.
Hierarchical clustering and heat maps. Temporal profiles (Time course or dose variation) if applicable.
Combined gene lists for cross comparisons.
Data mining for specified gene lists.
Analysis Report with methodology and summary of gene lists.
4. Functional Analysis: Gene Ontology classification and ranking,
Canonical pathway classification,
Any other gene lists supplied or specified.
5. Documentation: Technical write-up of analysis procedure.
Figures and Tables for presentation or publication.

Although these are routine steps, every project is expected to be novel with complex analysis schemes and variations to fit to specific requirements.  These can be addressed in the definition of the project or at any time during analysis.

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