Omics data can be uploaded by two ways in MetExplore:
Mapping can be performed in all biological objects stored in a metabolic network (pathways, reactions, metabolites, enzymes, gene products and genes). Select the type of the biological objects you want to map in the "Object" menu in the mapping grid.
Then, in the menu "Element" select the feature of the objects which will be used to identify them.
Each biological object can be mapped thanks to its name or its identifier.
For metabolites, two additional features are available for the mapping: the Inchi code and the monoisotopic mass. In the latter case, the user
can indicate the allowed error in ppm in the menu below the mapping grid.
The mapping default mode is the "one mapping mode". In this mode, only one mapping is done. This mode is used to simply map a list of objects (one column) with associated single numerical values (two columns) or to compare the same network in different conditions (multiple columns). Mapping and pathway enrichment will be performed for all elements in the first column, irrespectively of the values in the different columns.
The "multi mapping" mode will produce one mapping for each column. In each
mapping, the objects for which the value is different from NaN will be tagged
as identified in the grid and pathway enrichment will be performed only on
these objects. Select "Perform one separate mapping for each column" to
activate this mode.
Input file for a multiple mapping. Two mappings will be created: one for
the Intestine condition and one for the Liver condition. In the Intestine
condition, metabolites that will mapped as identified will be those that
have a value different from NaN in the Intestine condition.
To launch MetaboRank you need to select "MetaboRank" in header "Omics" menu.
After it you have do do a mapping of metabolites to select your fingerprint.
Then you can launch MetaboRank.
This analysis return Page rank and Chei rank of each metabolite of the network.
Launch MetaboRank
The results will appear in the Jobs grids when they will be finished.
To get the result click on result button in job tab in side component.
Get MetaboRank results
MetaboRank allows to use fold change as weight in the random walk algorithm.
To do that you have to do a mapping of metabolites with a fold change condition to map fold change on our fingerprint
and to select the corresponding condition in the MetaboRank form.
So metabolites near than metabolite of the fingerprint with big fold change could best recommendation.
This analysis return Page rank and Chei rank of each metabolite of the network.
In the metabolite grid, a new column will be displayed with a three sub columns:
In order to have intuitive representation of MetaboRank, MetExplore provides an interactive scatter plot.
MetaboRank results in scatter plot
It allows to :