These models enable us to exploit a different form of visual context, based on the co-occurrence analysis of patches in the whole image rather than on the more traditional spatial relationships.
This interpretation of lists and entries has been applied in the co-occurrence analysis of published gene expression signatures [35].
Namely, NetCutter can be used to perform co-occurrence analysis of genes or list derived from the same bipartite graph.
Co-occurrence analysis of transcription factor binding motifs has been carried out in a variety of slightly differing ways in a wide range of organisms, including humans.
Co-occurrence analysis of TF binding sites was chosen to achieve higher specificity in selecting potentially regulated promoter regions in foreground and background sets than is possible by considering individual PWMs only.
Co-occurrence analysis of data represented as bipartite graphs permits visualizing the structure of the bipartite graph either as communities of list entries (genes) or as communities of lists (PubMedID_ListID) in co-occurrence networks.
The co-occurrence analysis of the PubLiME data set published previously [35] identified 5 major network communities of genes with consistent functional annotations that are deregulated in cancer related gene expression signatures.
Furthermore, co-occurrence analysis of more than two entities can be performed using the same statistical model, which leads to increased signal-to-noise ratios, robustness towards noise, and the identification of implicit relationships between co-occurring entities.
Since the gene communities identified in gene co-occurrence analysis reflect the structure inherent in the bipartite graph (which is not affected by reversing the list-entry order), co-occurrence analysis of the reversed bipartite graph will result in PubMedID_listID communities that reflect the same underlying structure in the bipartite graph.
Co-occurrence analysis of microbial taxa from 43 household digesters in this study suggested strong within- and between-domain correlations between different groups of microorganisms within the digesters.
Previously, we have reported co-occurrence analysis of published gene expression signatures collected in the PubLiME repository (Finocchiaro et al. 2005; Finocchiaro et al. 2007).
