Microarray analysis techniques
are used in interpreting the data generated from experiments on DNA, RNA, and protein microarrays
, which allow researchers to investigate the expression state of a large number of genes - in many cases, an organism's entire genome
- in a single experiment. Such experiments generate a very large volume of genetic data that can be difficult to analyze, especially in the absence of good gene annotation.
Microarray data analysis involves several distinct steps, as outlined below. Changing any one of the steps has the potential to change the outcome of the analysis, so the MAQC Project was created to identify a set of standard strategies. Companies exist that use the MAQC protocols to perform a complete analysis.
Creating raw data
Most microarray manufacturers, such as Affymetrix
and Agilent, provide commercial data analysis software with microarray equipment such as plate readers.
Depending on the type of array, signal related to nonspecific binding of the fluorophore can be subtracted to achieve better results. One approach involves subtracting the average
signal intensity of the area between spots. A variety of tools for background correction and further analysis are available from TIGR, and Agilent (GeneSpring).
Entire arrays may have obvious flaws detectable by visual inspection, pairwise comparisons to arrays in the same experimental group, or by analysis of RNA degradation. Results may improve by removing these arrays from the analysis entirely.
Visual identification of local artifacts, such as printing or washing defects, may likewise suggest the removal of individual spots. This can take a substantial amount of time depending on the quality of array manufacture. In addition, some procedures call for the elimination of all spots with an expression value below a certain intensity threshold.
Aggregation and normalization
Comparing two different arrays, or two different samples hybridized to the same array generally involves making adjustments for systematic errors introduced by differences in procedures and dye intensity effects. Dye normalization for two color arrays is often achieved by local regression
. LIMMA provides a set of tools for background correction and scaling, as well an option to average on-slide duplicate spots.
Raw Affy data contains about twenty probes for the same RNA target. Half of these are "mismatch spots", which do not precisely match the target sequence. These can theoretically measure the amount of nonspecific binding for a given target. RMA is a normalization approach that does not take advantage of them, but still must summarize the perfect matches through median polish.. Quantile normalization, also part of RMA, is one sensible approach to normalize a batch of arrays in order to make further comparisons meaningful.
The current Affymetrix MAS5 algorithm, which uses both perfect match and mismatch probes, continues to enjoy popularity and do well in head to head tests.
Identification of significant differential expression
Many strategies exist to identify which array probes show an unusual level of over expression or under expression. The simplest one is to call "significant" any probe that differs by an average of at least twofold between treatment groups. More sophisticated approaches are often related to t-tests
or other mechanisms that take both effect size and variability into account. Curiously, the p-values associated with particular genes do not reproduce well between replicate experiments, and lists generated by straight fold change perform much better.This represents an extremely important observation, since the point of performing experiments has to do with predicting general behavior. The MAQC group recommends using a fold change assessment plus a non-stringent p-value cutoff, further pointing out that changes in the background correction and scaling process have only a minimal impact on the rank order of fold change differences, but a substantial impact on p-values.
Commercial systems for gene network analysis such as Ingenuity and Pathway studio create visual representations of differentially expressed genes based on current scientific literature. Non-commercial tools such as GenMAPP
also aid in organizing and visualizing gene network data procured from one or several microarray experiments. A wide variety of microarray analysis tools are available through Bioconductor
written in the R programming language
. The frequently cited SAM Excel module and other microarray tools are available through Stanford University. Another set is available from Harvard and MIT.
Specialized software tools for statistical analysis to determine the extent of over- or under-expression of a gene in a microarray experiment relative to a reference state have also been developed to aid in identifying genes or gene sets associated with particular phenotypes
. One such method of analysis, known as Gene Set Enrichment Analysis (GSEA), uses a Kolmogorov-Smirnov
-style statistic to identify groups of genes that are regulated together . This third-party statistics package offers the user information on the genes or gene sets of interest, including links to entries in databases such as NCBI's GenBank
and curated databases such as Biocarta and Gene Ontology
. Related system, PAINT and SCOPE performs a statistical analysis on gene promoter regions, identifying over and under representation of previously identified transcription factor