However, genes in cluster C had lower expression levels in pupal stages than those in cluster B. Although well organized expression patterns were shown in clusters B and C, exceptions were still found at several stages.
Although the tumour cell density of Bcl-2, p53, Bax, PCNA and TUNEL positivity correlated with patient survival, a spatially organized expression pattern was further recognized in stroma-poor differentiating tumours.
Interestingly, the reverse situation was observed in MCF7 cell system, in which the organized expression of Par3 and Lgl2 containing cell polarity complexes of parental cells (Fig 4B, h,j and insets) was fully lost in MCF7-LOXL2 cells (Fig 4B, g,i).
Given the large number of dynamically expressed genes in the hyperoxia groups, we sought to organize the expression data on the basis of biological processes.
Key to these results was that the coexpression network helped organize the expression traits into coherent, highly interconnected modules reflecting the biological processes at play in the tissue.
In particular evidence from lesion analysis studies suggests that the MPFC and related limbic and striato-pallido-thalamic structures organize emotional expression.
In this way, gene set testing can simplify and organize differential expression analyses by focusing attention on larger and more biologically meaningful processes than individual genes.
For example, structural biologists use The Protein Data Bank to store protein structures (4), geneticists use GenBank to share genomic sequences (5) and genomics researchers use the Gene Expression Omnibus to organize gene expression profiles (6) among many experimental databases routinely used in biology.
To further evaluate our microarray data, GenMAPP and MAPPFinder software were used to organize gene expression data into MAPPs (microarray pathway profiles) that represent specific biological pathways and functionally grouped genes, based on the GO system.
organize the expression data into a multiweighted coexpression network that is able to better highlight relationships among nodes compared to single-weighted networks, and analyze the multi-weighted network in order to identify regions of the network with interesting topological properties that may highlight relevant genes for the modeled phenomenon.
