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Start:
#contents
//-------------------
// MBGD Genomaple
//-------------------
* MBGD Genomaple [#j10c3e8d]
//-------------------
// Genomaple Results Page
//-------------------
** 1.1 Genomaple Results Page [#de3ba3d7]
The Genomaple Results Page presents the results of Genoma...
#ref(MBGD/Genomaple/genomaple_010.png,left,wrap,Genomaple...
This table provides the following information and functio...
+ ''Species Display List'':
~
A list of species to display. You can hide a species by u...
+ ''Module Filtering'':
~
If checked, modules absent in all target species (i.e., w...
+ ''CSV Download'':
~
Download the results of the Genomaple calculations in CSV...
+ ''Module Comparison'':
~
Clicking a module ID opens the Module Comparison Page in ...
+ ''MCR Table'':
~
A table showing the MCR% of each module for each target s...
+ ''Cross-Reference Settings'':
~
Modify the conditions for cross-referencing between KEGG ...
+ ''Genomaple Results Management'':
~
Navigate to the Genomaple results management page.
+ ''MBGD-KO Mapping Management'':
~
Navigate to the MBGD-KO cross-reference management page.
*** Recalculating MCR and Q-Value [#g19bea87]
In MBGD, the MCR and Q-Value for each module of each spec...
To adjust conditions, select option 6 to display the ''MB...
#ref(MBGD/Genomaple/genomaple_020.png,left,wrap,MBGD-KO C...
It takes approximately 20 seconds per species to calculat...
+ ''Only MCR Recalculation'':
~
Recalculates only the MCR and displays the results withou...
+ ''MCR and Q-Value Recalculation'':
~
Recalculates both MCR and Q-value and saves the results t...
+ ''MCR and Q-Value Force Recalculation'':
~
Ignores saved results and recalculates both MCR and Q-val...
*** Genomaple Results Management Page [#q346d7ea]
After modifying the MBGD-KO cross-reference conditions, y...
#ref(MBGD/Genomaple/genomaple_030.png,left,wrap,Genomaple...
+ ''Delete Calculation Results'':
~
Select the calculation results and click the "Delete" but...
+ ''Download Calculation Results'':
~
Click the "Download" button to save the calculation resul...
+ ''Upload Calculation Results'':
~
Select a calculation result file and click the "Upload" b...
Results are managed per species and cross-reference condi...
*** MBGD-KO Cross-Reference Management Page [#ve694f96]
In some cases, no corresponding MBGD ortholog group is id...
• 1.3 Mapping KO to MBGD
~
• 1.4 Homology Search
~
• 1.5 Viewing a Tree Diagram
~
You can use ''Homology Search'' to create a mapping table...
#ref(MBGD/Genomaple/genomaple_040.png,left,wrap,Link to M...
The MBGD-KO Cross-Reference Management Page allows you to...
#ref(MBGD/Genomaple/genomaple_050.png,left,wrap,MBGD-KO c...
+ ''Go to the "MBGD-KO Cross-Reference Registration" Page...
~
Modify the mappings manually.
+ ''Go to the "Clustering Tree Diagram" Page'':
~
View the clustering tree diagram showing subclusters crea...
+ ''Go to the "Search Results for Alternative Genes" Page...
~
Display the results dialog for the alternative gene searc...
+ ''Delete Stored Mappings'':
~
Remove the stored mapping between the KO and the locus ta...
+ ''Download Cross-Reference Information'':
~
Save the cross-reference information file to your device.
+ ''Upload Cross-Reference Information'':
~
Upload a previously downloaded cross-reference informatio...
//-------------------
// Module Comparison Page
//-------------------
** 1.2 Module Comparison Page [#v6973604]
The Module Comparison Page, accessible via the Genomaple ...
#ref(MBGD/Genomaple/genomaple_060.png,left,wrap,Module Co...
The functions of each element on this page are as follows:
+ ''Module ID'':
~
Click this link to open the KEGG module information page ...
+ ''Download Comparison Information'':
~
Export the comparison information to a CSV file.
+ ''Genome Layout Page'':
~
Open the Genome Layout Page in a separate window.
+ ''Module Structure Diagram'':
~
Open the module structure diagram.
+ ''Search for Alternative Genes'':
~
Display a search form to find alternative genes.
+ ''Species Display Options'':
~
Show a form to toggle the visibility of species and chang...
+ ''Check All Species'':
~
Select all species for display.
+ ''Highlight KOs on the Module Structure Diagram'':
~
Highlight the KOs of the selected species on the Module S...
+ ''KO ID'':
~
The identifier of a KO, consisting of each step in the KE...
~
#ref(MBGD/Genomaple/genomaple_061.png,left,wrap,image,60%)
+ ''MBGD cluster ID'':
~
MBGD cluster ID is displayed along with the overlapping p...
~
#ref(MBGD/Genomaple/genomaple_062.png,left,wrap,image,60%)
+ ''Ortholog Table'':
~
The locus tags of genes belonging to each MBGD ortholog g...
+ ''MBGD-KO Cross-Reference Conditions'':
~
Define the conditions for the MBGD-KO cross-reference. If...
#ref(MBGD/Genomaple/genomaple_070.png,left,wrap,Module Co...
~
~
+ ''Display Module Structure Diagram'':
~
The KOs of the checked species are highlighted in red on ...
+ ''Search for Alternative Genes'':
~
Perform a search for alternative genes associated with th...
+ ''Toggle Species Display'':
~
Use the checkboxes to show or hide species. You can also ...
//-------------------
// MBGD-KO Cross-Reference Conditions
//-------------------
** 1.3 MBGD-KO Cross-Reference Conditions [#yb0e2203]
The MBGD-KO cross-reference table defines the relationshi...
#ref(MBGD/Genomaple/genomaple_080.png,left,wrap,Table 1 R...
In the following example, the cross-reference is defined ...
#ref(MBGD/Genomaple/genomaple_090.png,left,wrap,An exampl...
In this example, the indication “K01601 (1)” in the KO co...
On the other hand, no cluster ID is associated with "K052...
#ref(MBGD/Genomaple/genomaple_100.png,left,wrap,KO inform...
From this page, you can see that the name of K05298 is "g...
Clicking the "(0)" next to "K05298 (0)" allows you to reg...
#ref(MBGD/Genomaple/genomaple_110.png,left,wrap,Searching...
Pressing the "Close" button will update the comparison ta...
#ref(MBGD/Genomaple/genomaple_120.png,left,wrap,Adding a ...
#ref(MBGD/Genomaple/genomaple_130.png,left,wrap,The added...
//-------------------
// Homology search
//-------------------
** 1.4 Homology search [#e56746a4]
When the Cluster ID corresponding to a KO is displayed as...
#ref(MBGD/Genomaple/genomaple_140.png,left,wrap,ClustsKO ...
Check the genes you want to display and click the "Select...
#ref(MBGD/Genomaple/genomaple_150.png,left,wrap,Display r...
//-------------------
// Clustering Tree Diagram
//-------------------
** 1.5 Clustering Tree Diagram [#h18a6e44]
Clustering Tree Diagram can be shown by clicking the link...
#ref(MBGD/Genomaple/genomaple_160.png,left,wrap,Clusterin...
+ ''Specify Tree Expansion Level'':
~
Set the level of hierarchy to which the tree diagram shou...
+ ''Internal (ancestral) node'':
~
Each internal node represents a set of genes that are des...
+ ''Tree Leaves'':
~
Represents individual genes. The gene name and the corres...
+ ''Search Within Tree Diagram'':
~
Search for text within the tree diagram.
+ ''Display Subcluster List'':
~
Show a list of subclusters.
+ ''Expand/Collapse All'':
~
Clicking ">" at each internal node expands all levels bel...
#ref(MBGD/Genomaple/genomaple_170.png,left,wrap,Sub-clust...
#ref(MBGD/Genomaple/genomaple_180.png,left,wrap,List of s...
//-------------------
// Genome Layout Page
//-------------------
** 1.6 Genome Layout Page [#re500569]
The Genome Layout Page can be accessed by clicking the "S...
#ref(MBGD/Genomaple/genomaple_190.png,left,wrap,Invoking ...
#ref(MBGD/Genomaple/genomaple_200.png,left,wrap,Genome La...
+ ''Specify Neighborhood Parameter'':
~
Define the neighborhood parameter (N). Neighborhood gene ...
+ ''Neighborhood Gene Cluster'':
~
This is an example of a cluster containing multiple genes...
The straight lines in the background represent sequence s...
+ ''Neighborhood Gene Cluster（Singleton）'':
~
Another neighborhood gene cluster consisting of a single ...
~
#ref(MBGD/Genomaple/genomaple_201.png,left,wrap,Genome La...
+ ''Chromosome/Contig'':
~
A dotted red square indicates that the enclosed segments ...
End:
#contents
//-------------------
// MBGD Genomaple
//-------------------
* MBGD Genomaple [#j10c3e8d]
//-------------------
// Genomaple Results Page
//-------------------
** 1.1 Genomaple Results Page [#de3ba3d7]
The Genomaple Results Page presents the results of Genoma...
#ref(MBGD/Genomaple/genomaple_010.png,left,wrap,Genomaple...
This table provides the following information and functio...
+ ''Species Display List'':
~
A list of species to display. You can hide a species by u...
+ ''Module Filtering'':
~
If checked, modules absent in all target species (i.e., w...
+ ''CSV Download'':
~
Download the results of the Genomaple calculations in CSV...
+ ''Module Comparison'':
~
Clicking a module ID opens the Module Comparison Page in ...
+ ''MCR Table'':
~
A table showing the MCR% of each module for each target s...
+ ''Cross-Reference Settings'':
~
Modify the conditions for cross-referencing between KEGG ...
+ ''Genomaple Results Management'':
~
Navigate to the Genomaple results management page.
+ ''MBGD-KO Mapping Management'':
~
Navigate to the MBGD-KO cross-reference management page.
*** Recalculating MCR and Q-Value [#g19bea87]
In MBGD, the MCR and Q-Value for each module of each spec...
To adjust conditions, select option 6 to display the ''MB...
#ref(MBGD/Genomaple/genomaple_020.png,left,wrap,MBGD-KO C...
It takes approximately 20 seconds per species to calculat...
+ ''Only MCR Recalculation'':
~
Recalculates only the MCR and displays the results withou...
+ ''MCR and Q-Value Recalculation'':
~
Recalculates both MCR and Q-value and saves the results t...
+ ''MCR and Q-Value Force Recalculation'':
~
Ignores saved results and recalculates both MCR and Q-val...
*** Genomaple Results Management Page [#q346d7ea]
After modifying the MBGD-KO cross-reference conditions, y...
#ref(MBGD/Genomaple/genomaple_030.png,left,wrap,Genomaple...
+ ''Delete Calculation Results'':
~
Select the calculation results and click the "Delete" but...
+ ''Download Calculation Results'':
~
Click the "Download" button to save the calculation resul...
+ ''Upload Calculation Results'':
~
Select a calculation result file and click the "Upload" b...
Results are managed per species and cross-reference condi...
*** MBGD-KO Cross-Reference Management Page [#ve694f96]
In some cases, no corresponding MBGD ortholog group is id...
• 1.3 Mapping KO to MBGD
~
• 1.4 Homology Search
~
• 1.5 Viewing a Tree Diagram
~
You can use ''Homology Search'' to create a mapping table...
#ref(MBGD/Genomaple/genomaple_040.png,left,wrap,Link to M...
The MBGD-KO Cross-Reference Management Page allows you to...
#ref(MBGD/Genomaple/genomaple_050.png,left,wrap,MBGD-KO c...
+ ''Go to the "MBGD-KO Cross-Reference Registration" Page...
~
Modify the mappings manually.
+ ''Go to the "Clustering Tree Diagram" Page'':
~
View the clustering tree diagram showing subclusters crea...
+ ''Go to the "Search Results for Alternative Genes" Page...
~
Display the results dialog for the alternative gene searc...
+ ''Delete Stored Mappings'':
~
Remove the stored mapping between the KO and the locus ta...
+ ''Download Cross-Reference Information'':
~
Save the cross-reference information file to your device.
+ ''Upload Cross-Reference Information'':
~
Upload a previously downloaded cross-reference informatio...
//-------------------
// Module Comparison Page
//-------------------
** 1.2 Module Comparison Page [#v6973604]
The Module Comparison Page, accessible via the Genomaple ...
#ref(MBGD/Genomaple/genomaple_060.png,left,wrap,Module Co...
The functions of each element on this page are as follows:
+ ''Module ID'':
~
Click this link to open the KEGG module information page ...
+ ''Download Comparison Information'':
~
Export the comparison information to a CSV file.
+ ''Genome Layout Page'':
~
Open the Genome Layout Page in a separate window.
+ ''Module Structure Diagram'':
~
Open the module structure diagram.
+ ''Search for Alternative Genes'':
~
Display a search form to find alternative genes.
+ ''Species Display Options'':
~
Show a form to toggle the visibility of species and chang...
+ ''Check All Species'':
~
Select all species for display.
+ ''Highlight KOs on the Module Structure Diagram'':
~
Highlight the KOs of the selected species on the Module S...
+ ''KO ID'':
~
The identifier of a KO, consisting of each step in the KE...
~
#ref(MBGD/Genomaple/genomaple_061.png,left,wrap,image,60%)
+ ''MBGD cluster ID'':
~
MBGD cluster ID is displayed along with the overlapping p...
~
#ref(MBGD/Genomaple/genomaple_062.png,left,wrap,image,60%)
+ ''Ortholog Table'':
~
The locus tags of genes belonging to each MBGD ortholog g...
+ ''MBGD-KO Cross-Reference Conditions'':
~
Define the conditions for the MBGD-KO cross-reference. If...
#ref(MBGD/Genomaple/genomaple_070.png,left,wrap,Module Co...
~
~
+ ''Display Module Structure Diagram'':
~
The KOs of the checked species are highlighted in red on ...
+ ''Search for Alternative Genes'':
~
Perform a search for alternative genes associated with th...
+ ''Toggle Species Display'':
~
Use the checkboxes to show or hide species. You can also ...
//-------------------
// MBGD-KO Cross-Reference Conditions
//-------------------
** 1.3 MBGD-KO Cross-Reference Conditions [#yb0e2203]
The MBGD-KO cross-reference table defines the relationshi...
#ref(MBGD/Genomaple/genomaple_080.png,left,wrap,Table 1 R...
In the following example, the cross-reference is defined ...
#ref(MBGD/Genomaple/genomaple_090.png,left,wrap,An exampl...
In this example, the indication “K01601 (1)” in the KO co...
On the other hand, no cluster ID is associated with "K052...
#ref(MBGD/Genomaple/genomaple_100.png,left,wrap,KO inform...
From this page, you can see that the name of K05298 is "g...
Clicking the "(0)" next to "K05298 (0)" allows you to reg...
#ref(MBGD/Genomaple/genomaple_110.png,left,wrap,Searching...
Pressing the "Close" button will update the comparison ta...
#ref(MBGD/Genomaple/genomaple_120.png,left,wrap,Adding a ...
#ref(MBGD/Genomaple/genomaple_130.png,left,wrap,The added...
//-------------------
// Homology search
//-------------------
** 1.4 Homology search [#e56746a4]
When the Cluster ID corresponding to a KO is displayed as...
#ref(MBGD/Genomaple/genomaple_140.png,left,wrap,ClustsKO ...
Check the genes you want to display and click the "Select...
#ref(MBGD/Genomaple/genomaple_150.png,left,wrap,Display r...
//-------------------
// Clustering Tree Diagram
//-------------------
** 1.5 Clustering Tree Diagram [#h18a6e44]
Clustering Tree Diagram can be shown by clicking the link...
#ref(MBGD/Genomaple/genomaple_160.png,left,wrap,Clusterin...
+ ''Specify Tree Expansion Level'':
~
Set the level of hierarchy to which the tree diagram shou...
+ ''Internal (ancestral) node'':
~
Each internal node represents a set of genes that are des...
+ ''Tree Leaves'':
~
Represents individual genes. The gene name and the corres...
+ ''Search Within Tree Diagram'':
~
Search for text within the tree diagram.
+ ''Display Subcluster List'':
~
Show a list of subclusters.
+ ''Expand/Collapse All'':
~
Clicking ">" at each internal node expands all levels bel...
#ref(MBGD/Genomaple/genomaple_170.png,left,wrap,Sub-clust...
#ref(MBGD/Genomaple/genomaple_180.png,left,wrap,List of s...
//-------------------
// Genome Layout Page
//-------------------
** 1.6 Genome Layout Page [#re500569]
The Genome Layout Page can be accessed by clicking the "S...
#ref(MBGD/Genomaple/genomaple_190.png,left,wrap,Invoking ...
#ref(MBGD/Genomaple/genomaple_200.png,left,wrap,Genome La...
+ ''Specify Neighborhood Parameter'':
~
Define the neighborhood parameter (N). Neighborhood gene ...
+ ''Neighborhood Gene Cluster'':
~
This is an example of a cluster containing multiple genes...
The straight lines in the background represent sequence s...
+ ''Neighborhood Gene Cluster（Singleton）'':
~
Another neighborhood gene cluster consisting of a single ...
~
#ref(MBGD/Genomaple/genomaple_201.png,left,wrap,Genome La...
+ ''Chromosome/Contig'':
~
A dotted red square indicates that the enclosed segments ...
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