Met­Ex­plore

Find­ing your path through net­work complexity

Met­Ex­plore Filters

Each panel (we will call them 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. Fil­ters may be spe­cific for each Met­Ex­plore ele­ment.

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.

BioSources

BioSource page allows to choose which biosource is gonna be used for the cur­rent session.

Select BioSource: allows select­ing the cur­rent BioSource

Com­part­ments

Metabo­lites are affected to com­part­ments in SBML mod­els. Thus reac­tions, espe­cially trans­port reac­tions, may have sub­strates in one com­part­ments and prod­ucts in another. When fil­ter­ing on com­part­ments we have thus two options: keep­ing only reac­tions involv­ing metabo­lites in the com­part­ment or keep­ing reac­tions with at least one metabo­lite in the selected compartment.

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.

Path­ways

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

Fil­ter with selec­tion: selec­tion of reac­tions and related ele­ments belong­ing to the selec­tion of pathways.

Reac­tions

Reac­tions have reg­u­lar fil­ters to select ele­ments involved in the selec­tion of reac­tions. In addi­tion, it is pos­si­ble to select reac­tions and put them in the cart for visu­al­iza­tion.

Copy selec­tion to cart: selected reac­tions will be added to the cart if they are not there already

Copy all to cart: all the reac­tions in the grid will be added to the cart if they are not there already

Fil­ter with selec­tion: fil­ter all the other grids based on the selec­tion of reactions.

Metabo­lites

Fil­ter with selec­tion: fil­ter all the other grids based on the selec­tion of metabolites.

Enzymes

Fil­ter with selec­tion: fil­ter all the other grids based on the selec­tion of Enzymes.

Pro­teins

Fil­ter with selec­tion: fil­ter all the other grids based on the selec­tion of Proteins.

Genes

Fil­ter with selec­tion: fil­ter all the other grids based on the selec­tion of Genes.