Brief instructions |
The layered representation:
Initially, the program is in the layered representation mode.
Every layer corresponds to a choice
of the threshold (resolution parameter).
The spheres represent the Modules (stable fixed points of the iterative scheme)
at each layer. (Summary of iterative scheme). Click on the spheres to view their gene and condition content in the windows on the right.
Every gene in the gene-window is linked to a page with some basic information about the gene.
Modules are arranged according to the correlation
between their condition scores. Correlated modules are close
to each other, while anti-correlated ones are at maximum separation.
The orange-blue bar underneath the module field shows the categorization of the module conditions according to mutant (orange)
and perturbation conditions (blue), cf. Fig. 2 in the paper. The conditions are ordered by their score (descending from left to right). The number of condition shown corresponds to the minimum p-value.
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The tree representation:
Click on the buttons ModuleTree and ModuleLayers to switch between the two representations. The tree representation is described in Fig.1b in the paper.
The boxes represent the Modules (stable fixed points of the iterative scheme).
Click on the boxes to view their gene and condition content in the windows on the right.
The depth of the tree can be selected from the drop-down menu or the two adjacent buttons.
The Tree Width and Tree Height buttons are used to zoom in and out of the tree. Full View adjusts the size of the tree to just fit the window.
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The module condition details:
Clicking on the white arrow in the bottom right corner of the module conditions window opens the module condition details.
Conditions are ordered by absolute score. They are categorized according to mutant conditions (orange), perturbation conditions (blue),
biological process (cyan) and unknown (gray).
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The gene condition details:
Clicking on the white arrow in the bottom right corner of the module conditions window opens the module gene details.
Genes are ordered by score. The ORFs are linked to the Saccharomyces Genome Database (SGD). For every gene, its localization, cellular role,
function, molecular environment and its viability are shown. The last column contains a one-line description summarizing the gene.
The pie chart shows the recurrence of the selected module in comparison to that of the other modules at the same resolution level.
The recurrence states how many random input sets converged into the module. This gives a measure of the attractive strength of the fixed point. The pie that is pulled out represents the recurrence of the selected module.
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Search:
This feature invokes a program on our server.
Modules can be searched for genes, conditions, or both.
Enter a keyword and click on Add. All genes/conditions in the dataset whose description contains the keyword are listed. The format is such that A+B+~C yiels all genes/conditions whose description contains both A and B and not C.
Click on genes or conditions to select them. Only modules that contain the selected genes/conditions are displayed.
The And/Or checkboxes indicate if a module is shown if it contains any of the genes/conditons (OR) or only if it contains all of them (AND).
Click on reset in the main window to display all modules again.
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