It is a difficult challenge to identify the functional effects of protein acetylation in specific pathways.
The results show that activity of drug effector and non-effector pathways as determined by genomic alterations influence drug sensitivity, and key targeting nodes in specific pathways may yield better therapeutic predictions by pathway-centric rather than gene-centric approaches.
Finally, the concept that efficacy should be defined by the activity of an endogenous ligand will be challenged by the discovery that some ligands act as 'super-agonists' in specific pathways or at certain receptor mutations.
To make faster and efficient the identification of mRNA targets common to more than one miRNA, and to identify new miRNAs modulated in specific pathways, a computer program identified as SID1.0 (simple String IDentifier) was developed and successfully applied in the identification of deregulated miRNAs in prostate cancer cells.
The whole analysis for each time-point, including details on number of miRNA and miRNA-mRNA interactions in specific pathways is available in online supplemental data.
This can be a set of proteins associated with a certain disease, involved in specific pathways, sharing other biological properties or transcripts that are differentially expressed in a condition of interest.
Finally, the use of operons, subsystems, and pathways to describe the array results avoids inappropriately building conclusions on the transcriptional changes of individual genes and thus better reflects biologically relevant perturbations in specific pathways.
Information processing refers to the transformation of signals [33], such as selective suppression of activation in specific pathways, which allows different sensory stimuli to initiate response in distinct sets of motor neurons.
We looked for enrichment in specific pathways among the significantly differentially-expressed genes when comparing wt versus mutant miR-122-expressing cells (using the Panther classification system http://www.pantherdb.org/).
The regression models we built showed that, in many cases, there is a continuum of effects influencing the molecular state of a target pathway and that, in specific pathways, (i.e. Gap junction and ErbB signalling pathways) toxicity is observed either above or below a given threshold of pathway activity (Figure 5).
Additionally, an important observation in our study was that the SNPs/genes that determine cluster formation in CD do not appear to group in specific pathways: eg TNFSF15 and IRGM, which explain cluster B (Figure 1B) are – to the best of our knowledge – not part of one and the same pathway.
