Extending the pathway analysis framework with a test for transcriptional variance implicates novel pathway modulation during myogenic differentiation.
BACKGROUND
We describe an extension of the pathway-based enrichment approach for analyzing microarray data via a robust test for transcriptional variance. The use of a variance test is intended to identify additional patterns of transcriptional regulation in which many genes in a pathway are up- and down-regulated. Such patterns may be indicative of the reciprocal regulation of pathway activators and inhibitors or of the differential regulation of separate biological sub-processes and should extend the number of detectable patterns of transcriptional modulation.


RESULTS
We validated this new statistical approach on a microarray experiment that captures the temporal transcriptional profile of muscle differentiation in mouse C2C12 cells. Comparisons of the transcriptional state of myoblasts and differentiated myotubes via a robust variance test implicated several novel pathways in muscle cell differentiation previously overlooked by a standard enrichment analysis. Specifically, pathways involved in cell structure, calcium-mediated signaling and muscle-specific signaling were identified as differentially modulated based on their increased transcriptional variance. These biologically relevant results validate this approach and demonstrate the flexible nature of pathway-based methods of data analysis.


BACKGROUND
The software is available as Supplementary Material.
Kemp
Daniel M
DM
Diabetes and Metabolism Disease Area, Novartis Institutes for BioMedical Research, Cambridge, MA 02139, USA.
Nirmala
N R
NR
Szustakowski
Joseph D
JD
D000818:Animals; D002454:Cell Differentiation; D003198:Computer Simulation; D018507:Gene Expression Regulation, Developmental / Q000502:physiology*; D014644:Genetic Variation / Q000235:genetics; D051379:Mice; D008954:Models, Biological; D032342:Muscle Cells / Q000166:cytology* / Q000378:metabolism*; D009124:Muscle Proteins / Q000378:metabolism; D032446:Myoblasts / Q000166:cytology* / Q000378:metabolism*; D015398:Signal Transduction / Q000502:physiology*; D014157:Transcription Factors / Q000378:metabolism*; D015533:Transcriptional Activation / Q000502:physiology
D009124:Muscle Proteins; D014157:Transcription Factors