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Even if there exist only a small number of motility modules, by combining different motility modules the cell could achieve a larger number of functions, e.g., combining protrusive motility modules on one side of the cell with retraction on the other gives rise to migration.
ClustEx is a two-step method for identifying the responsive gene modules by combining gene expression and interaction information.
There is an extensive body of literature on identifying cis-regulatory modules by combining a variety of data [ 1- 7].
The gene modules, by combining the results from GO, gene networks, and pathway analysis, were selected for further validation.
We have developed an integrative approach to identify HCV infection-associated miRNA-mRNA regulatory modules by combining paired miRNA and mRNA expression data and computational target prediction.
We successfully predicted five new cis-regulatory modules by combining binding site identification with sequence conservation and compared these to unsuccessful predictions from a related approach not utilizing sequence conservation.
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New long-term prediction module by combining the deharmonization predictor and the harmonic compensation filter has been proposed.
For the in silico design, we use a modeling framework which takes into account the limitations imposed by finite pools of resources; we synthesize the differentiator module by combining genetic regulatory parts which realize basic input/output functions such as a gain, integrator and signal difference.
(We note that there have been several studies that focused on understanding the dynamics of phospho-/dephosphorylation of this MAPK cascade module by combining in silico modeling with experimental data [19] [23]).
The TFs and their target genes were identified and organized into a module by combining comparative promoter analysis, gene expression data and known gene interactions.
Le et al. (2013) designed a iterative learning framework of protein interaction-based microRNA modules (PIMiM) by combining sequence, expression and interaction data, which can perform better than previous methods (including SNMNMF) [ 16].
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