There were no gene sets in the down regulated analysis that had an ambiguous interpretation and thus none had to be analyzed through EASE.
Additional file 8: a. Cluster analysis for Erlotinib Sensitive vs. regulated analysis using DAVID software.
The differentially regulated analysis for VPA (compared with the control) resulted in 256, 6 and 1 human miRNAs at ±1.5-fold change (Supplementary Table S3) for VPA, SAHA and TSA, respectively.
The Hypoxia gene set obtains rank 6 in the down regulated enrichment analysis.
In order to confirm the microarray results, ten genes were chosen (five up-regulated and five down-regulated) for analysis using quantitative real time PCR (Q-PCR).
The down-regulated gene analysis also highlighted a network linked to cell to cell signalling and cellular movement function, reflecting an impact of these gene modulations on cell motility and invasiveness (network 8, down-regulated genes, Table 7).
Hormone-regulated protein analysis showed that several proteins were regulated by cytokinin (Fig. 4).
Most importantly, the KSR1-regulated phosphoproteomic analysis has identified phospho-DBC1 as a potential connection to its modulation of p53 transcriptional activity here.
Involvement of Tpl2 in lung inflammation has been only indirectly demonstrated, since Tpl2 was found up-regulated in a proteome analysis of lung tissues from rats exposed to cigarette smoke [39], and mice lacking Tpl2 had reduced lung inflammation in a model of acute pancreatitis [31].
Interestingly, this gene was identified as the first gene up-regulated in a transcriptome analysis of hypoxic neuroblastoma cells, another neural-crest derived tumor that shares a number of features with PH/PGL [27].
In almost all categories a similar number of genes were up- as well as down-regulated, making a further analysis more challenging.
