Compartment Legendreferences where applicable.
Format Dataoption. Metaboverse expectes confidence intervals for each comparison to be formatted as:
[ [0.9, [[21.5761801, 21.7571531], [24.3988067, 25.6011932]]], [0.95, [[21.6215126, 21.7118207], [24.6999961, 25.3000038]]], [0.99, [[21.6576415, 21.6756917], [24.9400369, 25.0599630]]] ]
Format Dataoption. Doing so will launch a new window where an unformatted datatable can be uploaded and the user can select the relevant samples to experimental or control groups for a single 2-condition comparison or multiple comparisons for time-course or multi-condition datasets. A description of the usage of this module can be found in the Data Formatting Help section.
For most consistent behavior, you should only use tab-delimited tables with the suffix
For most consistent behavior, you should only symbolize a decimal with a period (.), NOT a comma (,).
If duplicate entity names are provided within a given transcriptomics, proteomics, or metabolomics data table, Metaboverse will ignore these elements.
_unmapped.txt. Data points could be unmapped for two reasons:
Reactome + the name of the unmapped speciesonline to see if the species goes by another name in Reactome, or if it is missing from the organism curation.
Output File Types¶
mvdb: This is the organismal curation file, containing the underlying network structure for the selected organism, as well as important node mapping information for connecting user-provided gene, protein, and metabolite measurements to the appropriate locations in the network.
mvrs: This is the completed organismal curation file, with your gene/protein/metabolite measurements mapped onto the network. You can load this file on the home page within the Metaboverse app to pick up where you left off in your analysis of the data.
mvdb, which contains the basic information needed to model the organism network without user data. This file can be saved for future usage if the user wishes to remodel data on that organism’s network without have to wait for all the necessary source files to download. This file can be provided in leiu of the organism name and file output on the appropriate page.
mvrsand contains the final network with the user data and user metadata stored. This file will allow for all downstream visualizations and analyses and can be reloaded on the main page of Metaboverse to quickly re-analyze a dataset. Clicking on the
Session Datatab in the menu on each page of Metaboverse will display the appropriate metadata for that particular model.
mvrsfiles can be saved to quickly access the organism curation or data model. For
v0.3.0bor earlier, these files ended in
Important Features of Metaboverse¶
Explorationpage, you can double-click on any reaction component and explore all connected reactions to this component across the total reaction network, not just the selected pathway. Additionally, you can select
All entitiesfrom the
Select a super-pathway...drop-down menu to select any component from the total network for this type of exploration.
Metaboverseinteractive app: The platform-independent app for visualizing and exploring data on the metabolic network. [code]
metaboverse-cli: The network curation and modeling utilities that form the back-end of the Metaboverse app. For each release of Metaboverse, OS-specific binaries are generated of the backend and incorporating into the GUI app. [code]