Take our Survey

Reference: Pearson CA, et al. (2013) Network class superposition analyses. PLoS One 8(4):e59046

Reference Help

Abstract


Networks are often used to understand a whole system by modeling the interactions among its pieces. Examples include biomolecules in a cell interacting to provide some primary function, or species in an environment forming a stable community. However, these interactions are often unknown; instead, the pieces' dynamic states are known, and network structure must be inferred. Because observed function may be explained by many different networks (e.g., [Formula: see text] for the yeast cell cycle process [1]), considering dynamics beyond this primary function means picking a single network or suitable sample: measuring over all networks exhibiting the primary function is computationally infeasible. We circumvent that obstacle by calculating the network class ensemble. We represent the ensemble by a stochastic matrix [Formula: see text], which is a transition-by-transition superposition of the system dynamics for each member of the class. We present concrete results for [Formula: see text] derived from Boolean time series dynamics on networks obeying the Strong Inhibition rule, by applying [Formula: see text] to several traditional questions about network dynamics. We show that the distribution of the number of point attractors can be accurately estimated with [Formula: see text]. We show how to generate Derrida plots based on [Formula: see text]. We show that [Formula: see text]-based Shannon entropy outperforms other methods at selecting experiments to further narrow the network structure. We also outline an experimental test of predictions based on [Formula: see text]. We motivate all of these results in terms of a popular molecular biology Boolean network model for the yeast cell cycle, but the methods and analyses we introduce are general. We conclude with open questions for [Formula: see text], for example, application to other models, computational considerations when scaling up to larger systems, and other potential analyses.

Reference Type
Journal Article | Research Support, U.S. Gov't, Non-P.H.S.
Authors
Pearson CA, Zeng C, Simha R
Primary Lit For
Additional Lit For
Review For

Interaction Annotations


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details about experiment type and any other genes involved in the interaction.

Interactor Interactor Type Assay Annotation Action Modification Phenotype Source Reference

Gene Ontology Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Gene Ontology Term Qualifier Aspect Method Evidence Source Assigned On Annotation Extension Reference

Phenotype Annotations


Increase the total number of rows showing on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table; click on the small "i" buttons located within a cell for an annotation to view further details.

Gene Phenotype Experiment Type Mutant Information Strain Background Chemical Details Reference

Regulation Annotations


Increase the total number of rows displayed on this page using the pull-down located below the table, or use the page scroll at the table's top right to browse through the table's pages; use the arrows to the right of a column header to sort by that column; to filter the table by a specific experiment type, type a keyword into the Filter box (for example, “microarray”); download this table as a .txt file using the Download button or click Analyze to further view and analyze the list of target genes using GO Term Finder, GO Slim Mapper, SPELL, or YeastMine.

Regulator Target Experiment Assay Construct Conditions Strain Background Reference