To perform this comparison using heterogeneous datasets from different measurement platforms and organisms, we developed a novel non-parametric methodology that can detect statistical significance of overlaps in ranked lists of genes, and estimate the number of genes with a common expression profile.
This step produces a subgroup of patients (individuals belonging to the shaded region of Figure 1(b)) with a common expression profile for gene-set A. Note that this subgroup is homogeneous in terms of the identified set of genes from the first step but can show distinct expression profiles between RY and RN on the other set of genes (e.g., genes marked in black).
Let-7a, in a cluster with let-7b, shared a common expression pattern as did miRNAs let-7e and miR-125a (3p & 5p) both in a cluster with miR-99b.
The data generated through this method allows predictions of function to be made for previously uncharacterized genes based on the observation that genes with similar function often show a common expression pattern.
This suggests the following further breakdown: Z = Zc + Zs, where Zc is a common expression component, with variance about 0.6, and Zs is a specific expression component, with variance about 0.04 for the amplified arrays and 0.14 for the unamplified arrays.
To 'hand someone his head' is a common expression, not normally associated with actual violence.
All chromosomes were seen to bear potential clusters (Additional file 4: Figure S3); however, closer examination revealed that genes within such clusters do not share a common expression profile, arguing against any functional organization and consistent with a previous study suggesting that P. falciparum lacks chromosomal domains with common expression profiles [ 1].
Cell lines clustered with a distinct common expression profile, and accordingly, the dendrogram united both fresh AML and CML samples in a separate common group.
Comparison between MG-132 and rotenone treatments showed only two time points with a common omi expression response namely, the control-level expression seen at 6H post-treatment, and the coincidental peak in expression at 12 hours.
Despite this important difference in terms of prognosis gene expression profiling identified mutated and UM CLLs as part of a shared disease process with a common gene expression signature.
Elsewhere, he devastatingly recalls that his reserved father was always "quiet yet genial, like a foreigner who could only respond with a few common expressions".
