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# XML Format ####
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Gene and regulator input files can be formatted as [simple lists](ListFile).
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However, to represent subclustering in a tree structure, XML can be used.
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The parent element is `ModuleNetwork`, it's children being `Module`s with an `id` attribute and an optional `name` attribute.
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A module has a `GeneTree` which contains a tree structure of `Child` elements, either with `node` attribute set to `internal` or `leaf`.
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Each child has an ordered set of `Gene` elements. A gene has a `name` attribute and an optional `alias` (symbolic name). Symbolic names could also be loaded from a simple mapping file at a later stage.
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Regulator data is formatted in a similar way, but uses `RegulatorTree` elements instead of `GeneTree`.
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Don't forget the XML declaration at the beginning of the file, to tell ModuleViewer the XML-parser should be used.
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Example:
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```
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<?xml version='1.0' encoding='iso-8859-1'?>
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<ModuleNetwork>
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<Module id="76" name="Cluster 76">
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<GeneTree>
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<Child node="leaf">
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<Gene name="YHR148W" alias="IMP3"/>
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<Gene name="YDR184C" alias="ATC1"/>
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<Gene name="YLR146C" alias="SPE4"/>
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<Gene name="YCR035C" alias="RRP43"/>
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<Gene name="YJR041C" alias="URB2"/>
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<Gene name="YKL014C" alias="URB1"/>
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<Gene name="YMR229C" alias="RRP5"/>
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<Gene name="YPR060C" alias="ARO7"/>
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</Child>
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</GeneTree>
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</Module>
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<Module id="24" name="YMR292W">
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<GeneTree>
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<Child node="internal">
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<Child node="leaf">
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<Gene name="YJL091C" alias="GWT1"/>
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</Child>
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<Child node="internal">
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<Child node="leaf">
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<Gene name="YDR222W"/>
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</Child>
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<Child node="leaf">
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<Gene name="YMR076C" alias="PDS5"/>
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<Gene name="YBL003C" alias="HTA2"/>
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<Gene name="YPR119W" alias="CLB2"/>
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<Gene name="YPL279C"/>
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<Gene name="YDR097C" alias="MSH6"/>
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<Gene name="YLR068W" alias="FYV7"/>
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<Gene name="YML052W" alias="SUR7"/>
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<Gene name="YPL227C" alias="ALG5"/>
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<Gene name="YAL059W" alias="ECM1"/>
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<Gene name="YLR049C"/>
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<Gene name="YIL158W" alias="AIM20"/>
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<Gene name="YDR302W" alias="GPI11"/>
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</Child>
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</Child>
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</Child>
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</GeneTree>
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</Module>
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</ModuleNetwork>
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```
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For "horizontal" subclustering (arranging a subset of conditions into a tree structure), one can use the `ConditionTree`.
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For this data, an extra element `NonTreeConditions` is introduced, to enable the user to place some conditions outside of the tree structure.
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The children of `Child` elements (and of `NonTreeConditions`) here are not `Gene` but `Condition`. Conditions ids are referencing to the position of
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the conditions in the original expression data matrix.
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```
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<?xml version='1.0' encoding='iso-8859-1'?>
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<ModuleNetwork>
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<Module id="206" name="YIL106W">
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<ConditionTree>
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<Child node="leaf">
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<Condition id="268"/>
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</Child>
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</ConditionTree>
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</Module>
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<Module id="23" name="YLR354C">
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<ConditionTree>
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<Child node="internal">
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<Child node="leaf">
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<Condition id="126"/>
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<Condition id="125"/>
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<Condition id="254"/>
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<Condition id="227"/>
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<Condition id="188"/>
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<Condition id="93"/>
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<Condition id="122"/>
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</Child>
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<Child node="leaf">
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<Condition id="272"/>
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<Condition id="263"/>
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<Condition id="267"/>
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<Condition id="258"/>
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<Condition id="53"/>
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<Condition id="260"/>
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</Child>
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</Child>
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</ConditionTree>
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<NonTreeConditions>
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<Condition id="165"/>
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<Condition id="47"/>
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<Condition id="232"/>
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</NonTreeConditions>
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</Module>
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</ModuleNetwork>
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``` |
