Thus, the module discovery algorithm searches for groups of inter-connected nodes that maximize the Q score.
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.
A motif-module discovery algorithm, CisModule [ 53], was used to detect motif patterns and the 5 most highly over-represented patterns were found (Table 6).
We would also like to highlight the difference between modularity measures, which quantify the modularity in a network whose modules have already been determined, and module-discovery algorithms, which partition a network into groups of nodes.
Often, module-discovery is performed by attempting to maximize a modularity measure, but in principle neither does a modularity measure imply an algorithm for module discovery, nor does a module-discovery algorithm necessitate a measure of modularity.
Here, the co-expression similarity S sj is the absolute value of the PCC between gene expression profiles × i, ×i (1) S ij = c o r (x i, x j ) Step 2. Module discovery using the weighted GN algorithm We applied the widely used weighted Girvan and Newman (GN) algorithm [ 20], a graph theory method based on edge betweenness algorithm.
Our approach consists of a method for rank-based network construction, a parameter-free graph partitioning algorithm for module discovery and a novel reference network-based metric for module evaluation.
To discover motifs that may underly changes in expression, we used the promoter regions for genes in three of the most interesting modules as input to motif discovery algorithms.
The iBBiG bi-clustering algorithm is optimized for module discovery in sparse noisy binary genomics data and can be used for meta-GSA of multiple genomics datasets, to discover modules: groups of phenotypes whose differential gene expression profiles are enriched in the same gene sets.
In addition, we integrated the SNBuilder and GeNa algorithms for subnetwork extraction and functional module discovery.
