The system also offers the possibility to compute the average expression value using recursion through the anatomic ontology by considering gene-expression strength from substructures.
Here we evaluate differences in the estrogen response kinetics by additionally considering gene expression enrichment at 12 hours of culture.
Limitations of this clinical trial include the short-duration of the intervention, examination of only single doses of lycopene and fish oil supplement, inability to assess the changes in the tumor tissue, inability to consider gene expression differences by cell-type (e.g., stromal vs. epithelial), usage of only a single housekeeping gene, and relatively small sample sizes.
Next, we considered gene expression data from the same in situ aged fibroblasts already published by Kalfalah and colleagues [ 10].
cMonkey has an internal scoring function that (without using BSCM) estimates bi-cluster quality by considering gene co-expression, known protein and genetic interactions, and the quality of common upstream binding motifs [ 3].
We identified 78 and 30 candidate genes associated with MD resistance, at 10 and 21dpi respectively, by considering genes having the same trend of expression change after MDV infection in lines 63 and RCS-M.
On the other hand, by considering genes with the same trend of expression change after MDV infection in lines 72 and RCS-M, we identified 78 and 43 genes at 10 and 21dpi, respectively, which may be associated with MD-susceptibility.
Another set of active TF-gene pairs was selected by network inference, by considering the gene expression signatures for those periods between GK and Wistar-Kyoto (WKY) rats.
The results indicate a general inhibitory effect of daunorubicin at both time points, as down regulated genes predominate over up regulated ones, and this trend was especially significant when considering genes whose expression changed by more than four-fold (lines "4X" and "0.25X" in Figure 1).
