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GenEpria Consulting Inc.
Microarray
and Multimodal Imaging Data Analysis Solutions |
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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