Sentence examples for module discovery method from inspiring English sources
We establish a new module discovery method, BEEM, which would be suitable for analysis of heterogeneous transcriptome data.
Here, we have introduced a new module discovery method, BEEM, to analyze sample subgroup-specific transcriptional programs which are functional only in subgroups of samples.
The idea is to provide one or several functionalities of specific interest and then to select all modules from the output of a module discovery method which are enriched with functionalities under consideration.
To overcome this limitation, we developed a new module discovery method termed BEEM (Biclusering-based Extraction of Expression Modules) in order to discover expression modules that are functional in a subset of tissues.
In order to demonstrate the benefits of our approach, we tested two module discovery methods, DECOB and DECOBRA, which arise from our framework.
We would finally like to point out that the design of strategies for comparison of clustering / module discovery methods which yield overlapping outputs is an active area of research (e.g. [23]).
Module discovery methods based on metabolic flux are either intractable at the genome scale or have more overlap between modules [ 15- 17].
Since we cluster the edges rather than nodes, the reported modules can overlap, which is an essential feature for module discovery methods.
Because of its superior performance to other methods in TF module discovery (Ding et al., 2013), we applied a modified version of ChIPModule to miRNA module candidate discovery.
Our approach consists of a simple but robust rank-based network construction method, a parameter-free module discovery algorithm and a novel reference network-based metric for module evaluation.
We compare the performance of our approach to previously described methods for motif and module discovery, and show that the pipeline supports detecting biologically relevant motif modules that are not easily discovered by other methods.
