Explore metabolic networks

Select a BioSource



In MetExplore, a BioSource corresponds to a metabolic network built for a strain, a cell line or a specific condition. You can select a BioSource by two ways: the "Selected BioSource" menu in the right panel or the BioSource grid. The BioSources are classified into 3 classes:

  • Public: these BioSources are readable by everyone but they can't be edited
  • Private: these BioSources correspond to metabolic networks , created or duplicated by the user
  • Project (when logged): these BioSources correspond to the metabolic networks stored in the open project

In the boxes of the "Selected BioSources", you can type some letters of the BioSource that you want to analyse to select it. Once a BioSource selected, the data grids are populated and information about the BioSource is displayed in the "Selected BioSource" menu.



Select a BioSource from the BioSource grid or from "Selected BioSource" menu in the right panel

MetExplore grids

Common features of MetExplore grids

Rearranging columns

In a MetExplore grid, you can rearrange columns as you want to facilitate data reading.
  • Reorder the columns. Keep clicking on the header of a column and move the column
  • Remove or add a column. Click on the right side of any column to show up the grid menu. In the submenu "Columns", check a column to make it visible or uncheck it to make it invisible

Sorting and filtering column data

  • Data of each column are sortable. Click once on the header of the column you want to sort or use the "Sort Ascending" or the "Sort Descending" buttons in the menu that appears after clicking on the right side of the column header.
  • Data of each column can be filtered. After clicking on the right side of the column header, enter some letters in the "Search" field". The data in the table will be filtered depending on the values contained in this column. Note that this filter is not propagated to the other grids. Use the propagating filters instead. To cancel a filter, erase the content of the "Search" field or right-click on the grid and click on "Delete Filter & Search".


By clicking on the right side of a column, a menu appears that enables to sort data, select columns which are visible or filter the data on the column

Selection of rows

Some MetExplore features are applied on a selection of rows. To select one row of a grid, just click on it. Click on CTRL-click to select several rows. Click on CTRL-A to select all the rows. Click on Maj-click to select successive rows.

Propagating filters

Excepting BioSource grid, each grid can filter the content of other grids by its rows that are selected. For this, right-click on the grid and click on "New filter on Selection". The propagating filter section provides more details about this.

BioSource grid

The grid "BioSources" lists all the BioSources available for the user. The Reload button at the right side enables to reload the list of all the BioSources.

Select a BioSource

Double-click on a row to select the corresponding BioSource.

Columns

To see and make visible all the columns of the grid, click on the right-side of a column and check or uncheck columns in the "Columns" menu. Columns visible by default:
  • id. MetExplore internal identifier of the BioSource. It is used for building an hyperlink to a specific biosource. It's also useful for communicating with MetExplore support team.
  • Name. Name of the BioSource, e.g. the name of the SBML model.
  • Organism. Organism of the BioSource often corresponding to the species name.
  • Source. The name of the database from which the BioSource has been created: *Cyc databases, KEGG, or individual SBML models
  • Strain. The strain of the organism, if available
  • Database type. The type of the database: BioCyc, kegg or others (SBML, created from scratch, etc...)
  • Publication. Reference of the publication where the metabolic network of the BioSource has been published
  • Nb Reactions
  • Nb Metabolites
  • Nb Genes
Columns hidden by default:
  • Creation Date.
  • Last Modification. Useful when the BioSource is shared between several users.
  • Complete Name. Just a concatenation of the Organism, the strain, the source database and the version.
  • Tissue. The tissue from which the BioSource comes from, if available
  • Cell Type. The cell type from which the BioSource comes from, if available
  • Version. The version of the BioSource.
  • Url. The url of the source database, if available. For *Cyc networks, this url is used to build the hyperlinks to original database.
  • Id in database. The identifier of the metabolic network in the original database. For *Cyc networks, this is used to build the hyperlinks to original database.
  • Status.
    • Public: these BioSources are readable by everyone but they can't be edited
    • Private: these BioSources correspond to metabolic networks , created or duplicated by the user
  • Metabolite-*
    • : % of metabolites containing a link to a chemical database (e.g. chebi, hmdb, etc...)

Group BioSources by columns

By default, the BioSources are grouped by organism name. But you can group BioSources by other characteristics listed in the GroupBy menu. This can facilitate the search for specific BioSources. You can click on "Expand all" to make visible all the BioSources in the groups or on "Collapse All" to hide them.



BioSource grid. Here BioSources are grouped by project.

Display info about a BioSource

In the grid, click on to display information in a new window about the corresponding BioSource: number of reactions, metabolites, etc... and generic information. From this window, you can copy the BioSource to get a private copy that you can edit and share.



BioSource information window.

Compartment grid

The grid "Compartments" lists all the compartments contained in a BioSource. It contains only two columns: the identifiers and the names of the compartments.



Compartment grid. Compartments of the BioSource recon2.

Pathway grid

Columns

The grid "Pathways" lists all the metabolic pathways contained in a BioSource. In the MetExplore data structure, metabolic pathways are associated to reactions. Then, a pathway can be considered as a collection of reactions. A reaction can be classified into several pathways.

By default, only three columns are visible in the grid: the information button, the identifier and the name.

For databases from BioCyc, a column with a link to the pathway page in the original BioSource is also displayed.
Three additional columns can be displayed (see here for displaying/hiding columns):
  • Nb reactions: number of reactions in the pathway
  • Nb reactions with Enz. number of reactions associated to an enzyme in the pathway
  • % Reactions with Enz. percentage of reactions associated to an enzyme in the pathway. Numbers in this column are colored considering their value from red (0%) to green (100%).
These additional columns are useful for evaluating the completness of the pathways. Indeed, reactions without enzymes can be considered as "pathway holes".

Information window

By clicking on , a window is displayed containing two grids:
  • A grid with all the reactions stored in the pathway
  • A grid with all the genes associated to the reactions in the pathway
Note that propagating filters can be activated from each grid.

When the BioSource is a private one, two panels are also displayed in this window: comments and votes. See here for further details.

Curation statistics

The button "Curation statistics" displays a window containing two plots:
  • A histogram displaying the number of pathways containing less than 25%, between 25 and 50%, between 50 and 75% and more than 50% of reactions associated to an enzyme.
  • The same plot but displaying the percentage of pathways in each category.




Pathway grid with additional columns, the information window and the curation statistics plot window.

Reaction grid

The grid "Reactions" lists all the reactions contained in a BioSource.

Columns

By default, the following columns are displayed:
  • Information button
  • Name
  • Identifier
  • E.C.: EC number describing the catalytic activity of the reaction
  • Reversible: checked if the reaction is reversible
  • Flux lower bound: Constraint on the lower bound of the reaction's flux (used in flux analyses)
  • Flux upper bound: Constraint on the upper bound of the reaction's flux (used in flux analyses)

Information window

By clicking on , a window is displayed containing these panels:
  • The equations of the reaction as described above
  • A graph showing the gene-protein-reaction links associated to the reaction. The legend can be displayed by clicking on "Show legend". The "Stop force" button stops the layout force algorithm. A double-click on a node displays a window displaying information about this biological object.
  • A grid listing all the pathways where the reaction is involved
  • A grid listing all the genes associated to the reaction
Note that propagating filters can be activated from each grid.

When the BioSource is a private one, two panels are also displayed in this window: comments and votes. See here for further details.

Tool Bar




Equations

The button "Equations" makes visible three additional columns:
  • Equation of the reaction with metabolite names
  • Equation of the reaction with metabolite chemical formulas
  • Equation of the reaction with metabolite identifiers

Aliases

The aim of aliases is to use custom names for each type of network element. These aliases are for example abbreviations which can be used for representation. The "Load aliases" button adds new columns to the grid. You can load a txt file with several columns: the first one with the identifier data, the others with aliases. Each additional column must have a different name (e.g. alias, alias2...). You can use these new columns for mapping.

Curation statistics

The button "Curation statistics" displays a window containing two plots useful for assessing the quality of the metabolic network reconstruction:
  • A plot showing the proportion of reactions with enzymes
  • A plot showing the proportion of reactions classified into a pathway




Reaction grid with formula columns, the information window showing the gene protein reaction links and the curation statistics plot window.

Metabolite grid

The grid "Metabolites" lists all the metabolites contained in the BioSource.

Columns

By default, these columns are displayed:
  • Name
  • Identifier
  • Formula
  • Compartment: in MetExplore, a metabolite is associated to only one compartment for facilitating modelling. If a metabolite is actually associated to several compartments, it will be duplicated in the MetExplore database.
  • Monoisotopic mass
  • Neutral Monoisotopic mass
  • Average mass
Two additional columns can be displayed (see here for displaying/hiding columns):

Information window

By clicking on , a window is displayed containing an image of the structure of the metabolite and its identifiers in several metabolic databases. Note that the completeness of this information depends on the BioSource and on the metabolite considered. Be careful, some of these links have been automatically added and can be not relevant.



Metabolite grid with the information window

Tool Bar




Aliases

The aim of aliases is to use custom names for each type of network element. These aliases are for example abbreviations which can be used for representation. The "Load aliases" button adds new columns to the grid. You can load a txt file with several columns: the first one with the identifier data, the others with aliases. Each additional column must have a different name (e.g. alias, alias2...). You can use these new columns for mapping.

Fuzzy search

The aim of fuzzy search is to easily find metabolite. The challenge is that metabolite can be wrote with abbreviations or special characters.
To do this search the Levenshtein distance is calculated as the minimum cost to transform the word M into P by performing the following elementary operations only:
  • substitution of a character of M by a character different from P ;
  • insertion (or addition) in M of a character from P ;
  • deleting an M character.

Substitution with a zero score:

  • cis abbreviation
  • trans abbreviation
  • acid form
  • ion form
  • coenzyme abreviation
  • charge
  • info
  • monosaccharides cyclic form
  • greek letters

Enzyme, gene product and gene grids

The grids "Enzymatic complexes", "Gene products" and "Genes" contains all only two columns: name and identifier.

MetExplore propagating filters



One of the main features of MetExplore is the ability to filter data grids from an other data grid. Each grid like the “Reac­tions” one allows apply­ing fil­ters. A fil­ter on a line or a set of lines will imply a selec­tion on the other grids. For instance, by fil­ter­ing on a Path­way, one can select all the reac­tions cor­re­spond­ing to this path­way and see them dis­played in the Reac­tions grid. Then, the filtering on reactions will activate the filtering on metabolites and enzymatic complexes. The filtering on metabolites will activate a selection of the compartments and the filtering on enzymatic complexes will filter the grid "Gene Products" and at last the grid "Genes".

Gen­eral usage:

  • Fil­ters can be accessed by right click­ing on lines
  • Mul­ti­ple selec­tion can be achieved by keep­ing the Ctrl key down
  • Delete fil­ter: this is present in all fil­ters and will remove cur­rent filter
The number of elements selected in each grid appears in the tab above the grid.

Compartments

Metabo­lites are affected to com­part­ments in MetExplore metabolic networks. Thus reac­tions, espe­cially trans­port reac­tions, may have sub­strates in one com­part­ment and prod­ucts in another. When fil­ter­ing on com­part­ments we have thus two options:
  • Fil­ter with selec­tion: this fil­ter will select reac­tions if they involve at least one metabo­lite in the selected compartment(s)
  • Fil­ter with­out trans­port: only reac­tions with sub­strates and prod­ucts in the com­part­ment are selected; transport reactions are filtered out

Pathways

Filtering on path­ways select reac­tions that are anno­tated as belong­ing to these path­ways. Note that some reac­tions may belong to one or more pathways.

Reactions

Filtering on reactions will select metabolites involved in these reactions, the enzymatic complexes associated to these reactions and pathways they belong to.

Metabolites

Filtering on metabolites will select reactions involving these reactions and the compartments which contain them.

Enzymatic complexes

Filtering on enzymatic complexes will select reactions associated to them and gene products forming them.

Gene Products

Filtering on gene products will select enzymatic complexes which contain them and genes that code for them.

Genes

Filtering on genes will select gene products coded by them.



Propagation of the filtering after filtering the pathway grid on the glycolysis