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Such high-level questions include: detecting differential expression in treatment and control tissues, gene function, pathway analysis, and changes in gene expression over time.
The iProClass database, designed to serve as a framework for data integration in a distributed networking environment, provides comprehensive descriptions of all proteins, with rich links to over 50 databases of protein family, function, pathway, interaction, modification, structure, genome, ontology, literature, and taxonomy.
Another critical commonly regulated pathway is LPS/IL-1 mediated inhibition of RXR function pathway.
LIPC, FASN, and APOB are primarily downstream genes of FXR/RXR signaling, which is also a part of LPS/IL-1mediated inhibition of RXR function pathway.
In the integrated model, however, the cell-cell and cell-substrate bonds were simulated using variables instead of constants, which can be regulated by the function pathway of the TGF-β1 COPASI model.
While a pathway is usually defined as a set of genes known to share a specific function, pathway boundaries are frequently difficult to assign, and methods that rely on such definition cannot discover novel pathways.
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One of SPIRE's primary assets is combining the results with data on protein function, pathways and protein expression from model organisms.
Another potential source of error comes from misspecification of immune function pathways.
However, antigen presentation/dendritic cell (DC) function pathways were not affected significantly during infection.
Intriguingly, the function, pathways, and targets affected by many of the miRNAs involved in nasopharyngeal tumorigenesis overlap.
Similarly, top molecular and cellular function pathways included cell cycle, gene expression, cell death, cellular growth and proliferation and cellular assembly and organization (p < 0.01 for all pathways).
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