![[PukiWiki]](image/header_title.png "[PukiWiki]")
#author("2024-12-17T14:32:13+09:00","default:mbgdadm","mbgdadm") [[MyMBGD]] #author("2024-12-17T14:33:54+09:00","default:mbgdadm","mbgdadm") #contents //------------------- // MBGD Genomaple //------------------- * MBGD Genomaple [#j10c3e8d] //------------------- // Genomaple Results Page //------------------- ** 1.1 Genomaple Results Page [#de3ba3d7] The Genomaple Results Page presents the results of Genomaple calculations for the specified species, displayed as a table of module completion ratios (MCRs) for each KEGG module. #ref(MBGD/Genomaple/genomaple_010.png,left,wrap,Genomaple Calculation Results Page,60%) This table provides the following information and functions: + ''Species Display List'': ~ A list of species to display. You can hide a species by unchecking it or change the display order by dragging the species codes. + ''Module Filtering'': ~ If checked, modules absent in all target species (i.e., with MCRs of 0 and Q-values of 0.5 or higher for all species) will be hidden. + ''CSV Download'': ~ Download the results of the Genomaple calculations in CSV format. + ''Module Comparison'': ~ Clicking a module ID opens the Module Comparison Page in a separate tab. + ''MCR Table'': ~ A table showing the MCR% of each module for each target species. Modules with a Q-value less than 0.25 have a red background, while those with a Q-value less than 0.5 have a blue background. + ''Cross-Reference Settings'': ~ Modify the conditions for cross-referencing between KEGG Orthology (KO) and MBGD ortholog groups, then recalculate the MCR and Q-value. + ''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 species are precomputed and stored in the database. This is bases on the MBGD-KO cross-reference defined in MBGD. Changing the MBGD-KO cross-reference conditions affects the KO composition, necessitating recalculations. To adjust conditions, select option 6 to display the ''MBGD-KO Cross-Reference Form'', where you can update the settings and recalculate. #ref(MBGD/Genomaple/genomaple_020.png,left,wrap,MBGD-KO Cross-Reference Configuration Form,40%) It takes approximately 20 seconds per species to calculate the MCR and about 4 minutes per species to calculate the Q-Value. To perform these modifications efficiently, the following three types of buttons are available: + ''Only MCR Recalculation'': ~ Recalculates only the MCR and displays the results without saving them. + ''MCR and Q-Value Recalculation'': ~ Recalculates both MCR and Q-value and saves the results to the browser's local storage. Reuses previously saved results under the same conditions if exist. + ''MCR and Q-Value Force Recalculation'': ~ Ignores saved results and recalculates both MCR and Q-value. *** Genomaple Results Management Page [#q346d7ea] After modifying the MBGD-KO cross-reference conditions, you can recalculate the MCR and Q-Value for each species and save the results in the browser's local storage. On this page, you can manage and organize these locally stored results. #ref(MBGD/Genomaple/genomaple_030.png,left,wrap,Genomaple Results Management Page,30%) + ''Delete Calculation Results'': ~ Select the calculation results and click the "Delete" button to remove them from the local storage. + ''Download Calculation Results'': ~ Click the "Download" button to save the calculation results stored in the local storage as a file. + ''Upload Calculation Results'': ~ Select a calculation result file and click the "Upload" button to register the results into the browser's local storage. Results are managed per species and cross-reference conditions. You can share results between browsers by downloading and uploading JSON files. *** MBGD-KO Cross-Reference Management Page [#ve694f96] In some cases, no corresponding MBGD ortholog group is identified for a KO in a KEGG module. To address this, MBGD provides several functions to assign MBGD ortholog groups to such KOs. For details, refer to the following sections: • 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 between genes (locus tags) and KOs as an alternative to the MBGD-KO mapping. In any case, users can view the customized MBGD-KO cross-references they have previously created by clicking the link to the ''MBGD-KO Cross-Reference Management Page''. #ref(MBGD/Genomaple/genomaple_040.png,left,wrap,Link to MBGD-KO Cross Reference Management Screen,40%) The MBGD-KO Cross-Reference Management Page allows you to view and modify the mappings set during each process. The following actions are available: #ref(MBGD/Genomaple/genomaple_050.png,left,wrap,MBGD-KO cross-reference management page,40%) + ''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 created by the user. You can modify the subcluster mappings directly on this diagram. + ''Go to the "Search Results for Alternative Genes" Page'': ~ Display the results dialog for the alternative gene search you selected and manually modify the mappings. + ''Delete Stored Mappings'': ~ Remove the stored mapping between the KO and the locus tag identified in the "Homology Search Results" page. + ''Download Cross-Reference Information'': ~ Save the cross-reference information file to your device. + ''Upload Cross-Reference Information'': ~ Upload a previously downloaded cross-reference information file. After selecting the file, click the Upload button to register it in the local storage of the current browser. This is useful for migrating information to another browser. //------------------- // Module Comparison Page //------------------- ** 1.2 Module Comparison Page [#v6973604] The Module Comparison Page, accessible via the Genomaple Results Page, displays an ortholog table containing genes associated with the specified KEGG module. The table allows you to compare the gene contents potentially related to the corresponding module across the specified species. #ref(MBGD/Genomaple/genomaple_060.png,left,wrap,Module Comparison Page,50%) The functions of each element on this page are as follows: + ''Module ID'': ~ Click this link to open the KEGG module information page in a separate tab. + ''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 change the display order. + ''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 Structure Diagram. When multiple species are selected, the KO color intensifies based on the number of overlapping species. To select only one species, hold the Shift key while clicking the desired species. + ''KO ID'': ~ The identifier of a KO, consisting of each step in the KEGG module. The number in parentheses indicates the total number of MBGD clusters corresponding to KOs registered in the MBGD-KO cross-reference table. Since the mapping can be modified by the "MBGD Cluster Search Conditions" in item (12), a corresponding cluster ID may not be found even if this number is greater than 0, resulting in "-1" being displayed. In such cases, you can relax the "MBGD Cluster Search Conditions" in item (12) to find the corresponding cluster ID. Clicking the link on the KO identifier opens the KO information page on the KEGG original site in a separate tab. Clicking the number in parentheses allows you to manually modify the MBGD-KO mapping. ~ #ref(MBGD/Genomaple/genomaple_061.png,left,wrap,image,60%) + ''MBGD cluster ID'': ~ MBGD cluster ID is displayed along with the overlapping pattern of the corresponding KO in the parentheses. Clicking on the cluster ID opens the MBGD Ortholog Cluster Page in a separate tab. Clicking the overlapping pattern in parentheses opens the Clustering Tree Diagram for the selected MBGD cluster in a separate tab. ~ #ref(MBGD/Genomaple/genomaple_062.png,left,wrap,image,60%) + ''Ortholog Table'': ~ The locus tags of genes belonging to each MBGD ortholog group are displayed for each species in the table. The background color indicates neighborhood clusters identified among the displayed genes in each genome; genes that are closely located on the same chromosome are assigned the same color. If a gene is isolated from other genes in the table, no background color is assigned. Clicking a locus tag opens the MBGD Gene Information Page in a separate tab. + ''MBGD-KO Cross-Reference Conditions'': ~ Define the conditions for the MBGD-KO cross-reference. If you edit the conditions and press the "Update" button, only the MCR values displayed in this table will be recalculated and updated. Note that the recalculation results are not saved. #ref(MBGD/Genomaple/genomaple_070.png,left,wrap,Module Comparison Page (Module Structure Diagram, with display settings open),50%) ~ ~ + ''Display Module Structure Diagram'': ~ The KOs of the checked species are highlighted in red on the diagram. + ''Search for Alternative Genes'': ~ Perform a search for alternative genes associated with the module. + ''Toggle Species Display'': ~ Use the checkboxes to show or hide species. You can also change the display order by dragging items in the list. //------------------- // MBGD-KO Cross-Reference Conditions //------------------- ** 1.3 MBGD-KO Cross-Reference Conditions [#yb0e2203] The MBGD-KO cross-reference table defines the relationship between KOs and MBGD clusters. These relationships can be classified as equivalent (KO ~ MBGD), supergroup (KO ⊃ MBGD), subgroup (MBGD ⊃ KO), or overlap (other partial overlapping relationships). Additionally, F-measure values are provided to quantify the degree of overlap between the two groups. Detailed definitions of these relationships are as follows: #ref(MBGD/Genomaple/genomaple_080.png,left,wrap,Table 1 Relationship between KO and MBGD ortholog group,40%) In the following example, the cross-reference is defined only when the relationship is equivalent or supergroup, and the F-measure ≥ 0.1. #ref(MBGD/Genomaple/genomaple_090.png,left,wrap,An example of MBGD-KO Cross Reference,60%) In this example, the indication “K01601 (1)” in the KO column signifies that the MBGD-KO cross-reference table contains one corresponding MBGD ortholog group for K01601. However, the corresponding MBGD ortholog group is displayed as -1, indicating that no valid MBGD group is found. This happens because the corresponding MBGD ortholog group does not meet the conditions specified under the MBGD-KO cross-reference conditions defined at the bottom of this page. In such a case, you can display all the corresponding MBGD ortholog groups in the original MBGD-KO cross-reference by selecting the subgroup option and setting the F-measure to 0 or higher. On the other hand, no cluster ID is associated with "K05298", even after the above adjustment of the cross-reference conditions. In such cases, you can search for MBGD ortholog groups and manually assign one that you believe corresponds to the KO. By clicking "K05298", you can see the original KEGG entry page is displayed as follows: #ref(MBGD/Genomaple/genomaple_100.png,left,wrap,KO information display,50%) From this page, you can see that the name of K05298 is "glyceraldehyde-3-phosphate dehydrogenase". You can search for MBGD ortholog group with this name and assign it to K05298. Clicking the "(0)" next to "K05298 (0)" allows you to register an MBGD-KO mapping. By entering a keyword of four or more characters in the Descr. field, you can search for MBGD cluster IDs containing that keyword. Once a matching cluster ID is found, select it and click the "Add" button to create the mapping, as shown below. #ref(MBGD/Genomaple/genomaple_110.png,left,wrap,Searching a new mapping between KO and MBGD cluster,50%) Pressing the "Close" button will update the comparison table with K05298 mapped to MBGD Cluster 8057, as shown below. This mapping information is saved in the browser's local storage. #ref(MBGD/Genomaple/genomaple_120.png,left,wrap,Adding a new mapping between K05298 and MBGD cluster 8054,50%) #ref(MBGD/Genomaple/genomaple_130.png,left,wrap,The added mapping is reflected on the comparison screen,50%) //------------------- // Homology search //------------------- ** 1.4 Homology search [#e56746a4] When the Cluster ID corresponding to a KO is displayed as "-1" (i.e. no corresponding MBGD ortholog group is found), you can perform a homology search to find potential genes corresponding to the KO. Clicking a Cluster ID displayed as "-1" will display potential genes for the corresponding KO in the Homology Search Results, as shown below. #ref(MBGD/Genomaple/genomaple_140.png,left,wrap,ClustsKO not compatible with,50%) Check the genes you want to display and click the "Select" button to add them to the module comparison table. #ref(MBGD/Genomaple/genomaple_150.png,left,wrap,Display result of the selected locus tag,50%) //------------------- // Clustering Tree Diagram //------------------- ** 1.5 Clustering Tree Diagram [#h18a6e44] Clustering Tree Diagram can be shown by clicking the link on the overlapping relationship between corresponding KO and MBGD ortholog group. The tree represents a phylogenetic tree of the target ortholog group on which each internal node represents the set of genes that are the descendent of it. #ref(MBGD/Genomaple/genomaple_160.png,left,wrap,Clustering Tree Diagram,50%) + ''Specify Tree Expansion Level'': ~ Set the level of hierarchy to which the tree diagram should expand. + ''Internal (ancestral) node'': ~ Each internal node represents a set of genes that are descendent of this node. For example, "40(32)" indicates that the ancestral node contains 40 genes, 32 of which correspond to the target KO (in this case, K15022). The higher the proportion of the target KO, the darker the background color. Clicking an internal node allows you to register it as a new subcluster. + ''Tree Leaves'': ~ Represents individual genes. The gene name and the corresponding KO are displayed within parentheses. + ''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 below the current one. Clicking again collapses them. #ref(MBGD/Genomaple/genomaple_170.png,left,wrap,Sub-clusters defined,50%) #ref(MBGD/Genomaple/genomaple_180.png,left,wrap,List of subclusters,50%) //------------------- // Genome Layout Page //------------------- ** 1.6 Genome Layout Page [#re500569] The Genome Layout Page can be accessed by clicking the "Show Genome Layout" button on the Module Comparison Page. It displays the arrangement of genes associated with the module on the chromosome.. #ref(MBGD/Genomaple/genomaple_190.png,left,wrap,Invoking Genome Layout Page form Module Comparison Page,50%) #ref(MBGD/Genomaple/genomaple_200.png,left,wrap,Genome Layout Page,50%) + ''Specify Neighborhood Parameter'': ~ Define the neighborhood parameter (N). Neighborhood gene clusters are defined as groups of genes related to the target module, where no two genes are separated by more than N consecutive unrelated genes. Modifying the parameter value and clicking the "Update" button will redefine the clusters based on the updated parameter. + ''Neighborhood Gene Cluster'': ~ This is an example of a cluster containing multiple genes associated with the module. Each arrow represents a gene: Colored Arrows are genes related to the target KEGG module, with colors assigned based on their MBGD ortholog group. Locus tags, KOs, and MBGD ortholog groups are displayed. Uncolored Arrows are genes unrelated to the module. Hovering over an arrow highlights genes belonging to the same ortholog group. Clicking an arrow opens the corresponding Gene Information Page in a separate tab. The straight lines in the background represent sequence segments where the genes are located. Genes on the same line belong to the same neighborhood gene cluster. These lines are painted with colors assigned to each neighborhood gene cluster, matching the background color of the locus tag on the Module Comparison Page. + ''Neighborhood Gene Cluster（Singleton）'': ~ Another neighborhood gene cluster consisting of a single gene. The straight line in the background is painted with the color assigned to the cluster. However, unlike ②, the background color of the locus tag on the Module Comparison Page is white. The arrow represents genes ~ #ref(MBGD/Genomaple/genomaple_201.png,left,wrap,Genome Layout Page,60%) + ''Chromosome/Contig'': ~ A dotted red square indicates that the enclosed segments are part of a consecutive sequence, such as a chromosome or contig.
