Met­Ex­plore

Find­ing your path through net­work complexity

Met­Ex­plore Content

  • BioSource: each meta­bolic net­work in Met­Ex­plore is stored as a BioSource. Note that a given organ­ism may cor­re­spond to sev­eral BioSources.
  • Com­part­ments: when the BioSource cor­re­sponds to an organ­ism with dif­fer­ent cel­lu­lar com­part­ments they can be specified.
  • Path­ways: Meta­bolic path­ways cor­re­spond to spe­cific meta­bolic func­tions (e.g. gly­col­y­sis), they may vary from one data­base to another, even for the same organ­ism. In Met­Ex­plore, a path­way is basi­cally a set of reactions.
  • Reac­tions: this is one of the main ele­ment of the BioSource. These reac­tions can then be selected and added to the cart in order to cre­ate meta­bolic networks.
  • Metabo­lites: mol­e­cules involved as sub­strate or prod­ucts of the reac­tions. Note that each metabo­lite may appear sev­eral times. Indeed, we con­sider dif­fer­ently the metabo­lites in the var­i­ous compartments.
  • Enzymes: the enzymes required to cat­alyze meta­bolic reac­tions. Note that a given enzyme may cat­alyze sev­eral reactions.
  • Pro­teins: pro­tein required to cre­ate enzymes. Note that there name and/​or iden­ti­fier often refer to sev­eral genes since they are often encoded by one or more genes.
  • Genes: gene cor­re­spond­ing to at least one meta­bolic func­tion. Note that the iden­ti­fied used is the one com­ing from the orig­i­nal data­base of the BioSource.
Biosource

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

name: com­mon given name of the biosource

organ­ism: the organ­ism for this biosource

source: nature of the ori­gin of the biosource, if it comes from a data­base (e.g. KEGG, Bio­Cyc) or a named recon­struc­tion (e.g. Recon2)

type: tells if the biosource was imported from an SBML or data­base (in that case data­base is name)

pub­lic: true if the biosource is pub­licly avail­able, false if it belongs to one ore sev­eral users

pub­li­ca­tion: it is pos­si­ble to attach ref­er­ences to biosource, for now they are given as a list of PMIDs (pubmed ids)

Com­part­ments

com­part­ment: abbre­vi­a­tion of the given com­part­ment (gen­er­ally cor­re­sponds to the com­part­ment iden­ti­fier in SBML file)

com­part­ment name: full name of the compartment

Path­ways

name: com­mon name of the path­way
dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

Reac­tions

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

name: com­mon name of the reaction

ec: Enzyme Com­mis­sion num­ber which can be used to retrieve enzy­matic func­tion of the reac­tion (for instance using ExPASY ser­vice). NA means that no num­ber is pro­vided for the reaction.

for­mule: pro­vides sub­strates, prod­ucts and sto­chiom­e­try of the reaction.

reversible: if checked it means that the reac­tion can hap­pen in both direc­tion. If not checked, it means reac­tion will hap­pen only in the direc­tion spec­i­fied by sub­strates and products.

lower­Bound: parme­ter used for Con­straint Based Mod­el­ling like Flux Bal­ance Analy­sis. It is the min­i­mum flux value that can be car­ried by the reaction.

upper­Bound: parme­ter used for Con­straint Based Mod­el­ling like Flux Bal­ance Analy­sis. It is the max­i­mum flux value that can be car­ried by the reaction.

Metabo­lites

name: com­mon name of the metabolite

chem­i­cal­For­mula: if avail­able, chem­i­cal for­mula of the compound

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

com­part­ments: com­part­ment where this metabo­lite can be found

weight: Mol­e­c­u­lar weight in Met­Ex­plore is the neu­tral mono­si­topic mass cor­rected with the charge of com­pounds. When pos­si­ble, we com­pute this mass based on the Inchi.

side com­pound: if checked it means that the metabo­lite will not be con­sid­ered in the visu­al­iza­tion nei­ther in graph computations.

Enzymes

name: com­mon name of the enzyme

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

Pro­teins

name: com­mon name of the protein

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element

Genes

name: com­mon name of the gene

dbIden­ti­fier: unique Met­Ex­plore iden­ti­fier for this element