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Microme data

Microme jamboree – June 27th 2011 - Genoscope

• Compounds• Reactions• Pathways • Genes / Genomes• Polypeptides / Proteins

• Metabolic networks

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Compounds / ReactionsChEBI : 28’306 molecular structures

Rhea : release 23 (June 2011)4’108 approved master reactions,

3’183 are linked to complete EC numbers. 267 transport reaction

3’667 chemical entities (small molecules)

Rhea cross-references: EcoCyc 1’050MetaCyc 3’312KEGG 3’276

Microme jamboree – June 27th 2011 - Genoscope

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Compounds / Reactions issuesDone:

Rhea – UniProt xrefs available (rel 23)

(Still) under developmentBulk submission tools (ChEBI, Rhea) Reactions with macromoleculesPolymerization reactions

Microme jamboree – June 27th 2011 - Genoscope

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Genes / ProteinsGenes / Genomes : EnsemblBacteria

Polypeptides : UniProt

Proteins :There is no reference resources for protein complexes- Protein complexes (EcoCyc / MetaCyc)- Gene associations (public metabolic networks)

Microme jamboree – June 27th 2011 - Genoscope

5Microme jamboree – June 27th 2011 - Genoscope

Microme specieshttp://www.ebi.ac.uk/seqdb/confluence/display/Microme/Accession+list

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Pathways

In its first release, Microme will focuse on EcoCyc / MetaCyc pathways

Microme/Reactome pathways

Microme jamboree – June 27th 2011 - Genoscope

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Metabolic networks

E.coli iAF1260B.subtilis iBsu1103A.baylyi iBaylyiP.aeruginosa iMO1056 paonew (WP3)P.putida ppunew (WP3)

Microme jamboree – June 27th 2011 - Genoscope

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iAF1260 metabolic network E.coli

129

856

374 Unreviewed reactions

Reviewed reactions with valid RHEA xreference

Reviewed reactions invol-ving lipidic-macromolecular compounds

1’359 biochemical reactions

Microme jamboree – June 27th 2011 - Genoscope

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Ppunew100629 metabolic network Pseudomonas putida KT2440

922

5543

829

2 3

Valid CHEBI ID ph 7.3ACP compounds (macromolecu-les)tRNA compounds (macromolecu-les)Proteins (macromoleculesLPS compounds; Not enough in-formation for 2D structure for-mulationOngoing submission (problems with final step of Submission; Error: Null caused by:Null)Alginate derivative compounds (not enough information)

TOBIN compounds / reactions mapped to KEGG

TOBIN compounds / KEGG compounds / ChEBI compounds

Microme jamboree – June 27th 2011 - Genoscope

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Ppunew100629 metabolic network Pseudomonas putida KT2440

iAF1260 internal reactions (1359 reactions)

Reaction mapping from Ppunew100629 network:

TOBIN / KEGG / Rhea651 TOBIN reactions mapped to KEGG

among them : 492 reactions are cross-referenced in Rheafull mapping : under progress

Microme DB

TOBIN / KEGG / Rhea / MetaCyc MaGE DB

Microme jamboree – June 27th 2011 - Genoscope

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Pseudomonas putida KT2440MaGE - PathoLogic

iAF1260 internal reactions (1359 reactions)

1’299 (gene,reaction) pairs1’119 distinct reactions (MetaCyc)

632 / 1’119 reactions are cross-referenced in Rhea647 Rhea reactions [NAD(P)]

487 MetaCyc reactions not mapped

Microme jamboree – June 27th 2011 - Genoscope

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Pseudomonas putida KT2440TOBIN – MaGE

UniProt proteome: 5’313 entries(pseudogenes – new predictions)

694 genes with links to MaGe & TOBIN

265 genes with links to TOBIN but not Mage

540 genes with links to MaGE but not TOBIN

Microme jamboree – June 27th 2011 - Genoscope

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Microme databases

3 Microme/Reactome dbs:microme_prerelease_eco_meta_cyc_14_5_iaf1260

EcoCyc + MetaCyc + curated data (met. networks)

microme_prerelease_eco_meta_cyc_14_5 EcoCyc + MetCyc

microme_prerelease_ecocyc_14_5_jamboree EcoCyc plus initial projections

Microme jamboree – June 27th 2011 - Genoscope