We demonstrate that this resilience to noise of "shallow" sequencing derives from a natural property, low dimensionality, which is a fundamental feature of gene expression data.
Our review also shows that although classic ANOVA and the t-test are widely applied to the analysis of gene expression data, fundamental statistical assumptions, such as the homogeneity of variances, are seldom mentioned.
While gene expression data indicates fundamental differences in cell invasion by merozoites, the question whether merozoites assemble an alternative moving junction machinery for invasion or invade enterocytes by an entirely different mechanism, e.g. based on membrane-zippering such as in Theileria [ 46] or Neospora [ 47], requires further investigation.
The analysis of large-scale gene expression data is a fundamental approach to functional genomics and the identification of potential drug targets.
The majority of approaches for analyzing time course gene expression data are based on the fundamental premise that over-populated motifs are indicative of significant events and thus searches for them as the main priority [9].
To obviate fundamental difference inherent in different array platforms, we focused mainly on gene expression data based on Affymetrix oligonucleotide arrays, particularly more advanced platforms such as U95Av2 or U133 series.
GUDMAP aims to provide a fundamental description of gene expression in the developing mouse GU system, generating gene expression data that will 'enable, facilitate and stimulate research' into understanding the GU system (McMahon et al., 2008).
To obviate fundamental difference inherent in different array platforms, we focused our analysis on gene expression data from NCI60 cell lines and primary tumors (Table 1) based on Affymetrix U95Av2 oligonucleotide array platform.
The fundamental difference between the two array platforms poses a technical barrier in integrative analysis of gene expression data based on these two different platforms.
Microarray analysis methods produce large sets of gene expression data that can be exploited for novel insights into the fundamentals of molecular biology research.
