What is a module?

Regulatory units (modules) in the Chlamy Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and a time-lagged correlation analysis to identify TRs controlling the changes on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.


Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the particular condition. On the right-hand side of the page we show the full trajectory of the dynamics of the module, called Model Expression Profile, explained below.


Module Expression Profiles

For the current module we plotted the expression values of the module along time in an ammonia starvation experiment [Boyle et al. 2012]. The thick black line represents the mean expression value for the members of the module. Specifically, it is the log2 fold change with respect to the initial conditions. The gray area specifies a region one standard deviation around the mean expression values. Finally, highlighted at the plot title, we show the first time at which the module mean expression is observed to be above the 2-fold change.



Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.


Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and #2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.



For each module, regulatory influences are listed under the regulators tab. These regulatory influences are identified based on temporal correlation of the expression changes.



Residual: is a measure of module quality. Mean module residual is smaller when the expression profile of the genes in the module is "tighter". So smaller residuals are usually indicative of better module quality.

Expression Profile: is a preview of the expression profiles of all the genes under subset of conditions included in the module. Tighter expression profiles are usually indicative of better bicluster quality.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module. Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 0.1 are generally indicative of significant motifs.

Genes: Number of genes included in the module.

Functions: We identify functional enrichment of each module by comparing to different functional categories such as Gene Ontology by using corrected hypergeometric tests. If the module is significantly enriched for any of the functions, this column will list these functions as an overview, linked to the appropriate GO term reference.