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The two remaining clusters assemble genes whose expression is modified by the treatment but not by aging (cluster C, Table S5), and genes modulated by aging but not by the treatment (cluster D, Table S6).
Interestingly, we found that genes which are preferentially upregulated upon either Etoposide (cluster 4) or Actinomycin D treatment (cluster 5) are nonetheless indiscriminately bound by p53 upon both treatments as shown for the indicated examples of the SerpinB5 and FGD3 genes for cluster 4 and the CDC42EP3 and PDE4C genes for cluster 5 (Figure 3C).
However some transcripts showed a bimodal expression pattern between 6 and 12 hours after LPS treatment (cluster 7, n = 257).
Genes involved in translation were down-regulated by DTT, but only after 4 h of treatment (Cluster 1 in Figure 4, Tables 2 and 3).
Genes whose expression increased with C. pneumoniae treatment (cluster 1) represented G-protein coupled signaling, viral myocarditis, antigen processing and presentation, and membrane genes.
The ketogenic diet and steroids were in the non-AED treatment cluster that was rated as showing improvement in communication and behavior, thereby verifying previous studies [ 38, 39].
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The control and PGPB treatment clustered together.
After this model treatment, clusters were found to keep their identities, and their structure and segregation state did not differ much from those in the initial free clusters.
The redband-only treatment clustered in distinctly different axis space, being most similar to the exclosure treatments.
The princess-only treatment clustered differently than these two treatments while the mixed-herbivore treatment showed large variation in community structure.
At the 4 h time point genes up-regulated after IFN-β treatment clustered with two GO biological processes, both involved in the host immune response.
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