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In blue = Isolated reactions in the Reactome pathway . Reproduces the situation in ECOCYC PowerPoint PPT Presentation


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Problem with generic compounds+Unconnected pathway in ECOCYC ( i.e. : ECOCYC: PWY-2161 = Folate polyglutamylation ) Problem in reaction compartment association in ECOCYC ( i.e. : ECOCYC: 2PHENDEG-PWY: Phenylethylamine degradation I)

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In blue = Isolated reactions in the Reactome pathway . Reproduces the situation in ECOCYC

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In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

  • Problemwithgenericcompounds+Unconnectedpathway in ECOCYC (i.e.: ECOCYC: PWY-2161 = Folatepolyglutamylation)

  • Problem in reactioncompartmentassociation in ECOCYC (i.e.: ECOCYC: 2PHENDEG-PWY: Phenylethylaminedegradation I)

  • Problemswithpathwaydiagramrepresentation: Multipleconnectivity of commonintermediates (H+, H2O, ATP, etc), whichdifficultspathwaydiagramvisualization (i.e.: ANARESP1-PWY: respiration (anaerobic))

  • Problemswithdifferentcytosol/cytoplasmcompartmentassociationforthesamecompound in differentreactions of thepathway = Twodifferententitiesforthesamecompound, generatingconnectivityproblems in thecorrespondingreactions (i.e.: ANARESP1-PWY: respiration (anaerobic))

  • Problemwithdifferentreferenceentitiesusedforthesamecompound in differentreactions = Connectivityproblem (i.e.: ECOCYC: PEPTIDOGLYCANSYN-PWY)

  • Problem of connectivitybetweensubpathways in superpathways (i.e.: ECOCYC: DENOVOPURINE2-PWY)

  • Problemwithdifferent CHEBI referenceentitiesforthesamecompound in differentreactions (i.e.: ECOCYC: OXIDATIVEPENT-PWY)

  • Additionalproblemwithlack of BIGG xreferences in ECOCYC reversible reactions


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: PWY-2161 = Folatepolyglutamylation: Problemwithgenericcompounds+Unconnectedpathway in ECOCYC

In blue = Isolatedreactions in theReactomepathway. Reproduces thesituation in ECOCYC


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Blue reactions in previousslide

FOLYLPOLYGLUTAMATESYNTH-RXN

RXN0-2921

FORMYLTHFGLUSYNTH-RXN

Genericreactionsdealingwithpolymers (addition of L-glutamatesubunitstotetrahydrofolateprecursors). Problems in ECOCYC reactions at compound ID forgenericcompounds


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

i.e.: FORMYLTHFGLUSYNTH-RXN: Samecompound ID forbothgenericcompoundsincluded in thereactiondespiterepresented as differentcompounds (n/n+1)

COMPOUND ID: FORMYL-THF-GLU-N

ECOCYC:FORMYL-THF-GLU-N = Classcompound

COMPOUND ID: FORMYL-THF-GLU-N

In micromerepository, thecorrespondingreactionshavethesamecompound as substrate and product in thepathwaydiagram


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Samecompoundentity as reactant and product


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Simple entity (CHEBI compound) as referenceEntity of thedefinedSet

DefinedSetentity in Microme

Howtosolvethisproblem in pathwaydiagrams??


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: 2PHENDEG-PWY: Phenylethylaminedegradation I:Problem in reactioncompartmentassociation in ECOCYC

Connectedreactions in ECOCYC pathwaydiagramdespitetheassociatedcompartmentisdifferent (periplasmicspace in firstreaction and cytoplasm in secondreaction). Thisyieldsunconnectedpathwaydiagrams in Micromerepository


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Unconnectedmetabolites


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Samereferenceentityforphenylacetaldehyde in bothreactions (CHEBI:16424) butdifferentcompartment = 2 differentdatabaseentities

Whatshouldbe done in this case???


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: ANARESP1-PWY: respiration (anaerobic):Problemswith:

Pathwaydiagramrepresentation: Multipleconnectivity of commonintermediates (H+, H2O, ATP, etc), whichdifficultspathwaydiagramvisualization

Differentcytosol/cytoplasmcompartmentassociationforthesamecompound in differentreactions of thepathway= Twodifferententitiesforthesamecompound, generatingconnectivityproblems in thecorrespondingreactions


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: ANARESP1-PWY: respiration (anaerobic)

Micromediagram: Multipleconnectionsbetweencommonmetabolitesdifficultspathwayrepresentation

ECOCYC diagram (linear)

H20 metabolite (6 reactionsassociated)


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

This can besolvedbyduplicatingthismetaboliteentities in thepathway editor of Reactomecuratortool(1 metaboliteentityforeachreaction in thediagram) Duplicatedentities conserve samedatabaseidentifier (same DB_ID)

InitialMicromediagram

EditedMicromediagram

2nd problem: Connectivity


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Samereferenceentity (CHEBI:29806) butdifferentcompartment (GO term) = 2 differententities = Connectivityproblem

Possiblesolution: Unification of cytosol/cytoplasmwith single GO compartment


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: PEPTIDOGLYCANSYN-PWY: Problemwithdifferentreferenceentitiesusedforthesamecompound in differentreactions = Connectivityproblem

Connectivityproblem

Unconnectedreactions in ECOCYC pathway (same case as firstexample of thepresentation)


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

DB_ID: 23436; RefEntity=CHEBI:61386

DB_ID: 45118; RefEntity=PubChemcompound


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Bothreactionscross-referenced in RHEA; RHEA reactionsconnectedthrough CHEBI:61386

RHEA:28375

RHEA:28388

Wrong RHEA xref (oppositedirection). Correctxreferenceis RHEA:28387 (In ObiWarehouse iAF1260:PAPPT3 and in RHEA, with RHEA:28387 xreferencedto ECOCYC reactions)


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Whythishappens (differentreferenceentityforthesamecompound in differentreactions)

Whatshouldwe do in this case??


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: DENOVOPURINE2-PWY: Superpathway of purinenucleotidesbiosynthesiswith 4 nestedpathways. Problem of connectivitybetweensubpathways

5-phospho-D-ribose-diphosphate (DB_ID:39069; PubChemreferenceEntity)

RHEA:14907; iAF1260:GLUPRT

Connectedpathwayswith RHEA reactions (through CHEBI:58592 in bothreactions)

PWY-6122

RHEA:23033; iAF1260:PRAIS

5-aminoimidazole ribonucleotide (DB_ID:45283; PubChemreferenceEntity)

Unconnectedpathways in Microme

5-aminoimidazole ribonucleotide (DB_ID:36474; CHEBI:58592 referenceEntity)

RHEA:19318; iAF1260:AIRC2

PWY-6123

RHEA:18447; Iaf1260:IMPC

Unconnectedpathways in Microme

IMP (DB_ID:1557; CHEBI:58053 referenceEntity)

IMP (DB_ID:13357; PubChemreferenceEntity)

IMP (DB_ID:13357; PubChemreferenceEntity)

RHEA:11709; iAF1260:IMPD

RHEA:15754; iAF1260:ADDS

PWY-6125

PWY-6126

Connectedpathways (PWY-6123/PWY-6125) with RHEA reactions (RHEA:18447-11709) through CHEBI:58053 in bothreactions)

Connectedpathways (PWY-6123/PWY-6126) with RHEA reactions (RHEA:18447-11709) through CHEBI:58053 in bothreactions)


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

ECOCYC: OXIDATIVEPENT-PWY: Problemwithdifferent CHEBI referenceentitiesforthesamecompound in differentreactions

Micromepathway

ECOCYC pathway

Unconnectedreactions


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

RHEA:12557

CHEBI:48928 as referenceentity; DB_ID:2367

RHEA:10117

CHEBI:58759 as referenceentity; DB_ID:5050

Both RHEA reactions uses CHEBI:58759 as 6-phospho-D-gluconate (majormirospecie at ph 7.3). CHEBI:48928 isthe CHEBI xreference of 6-phospho-D-gluconate in ECOCYC, whichiswrong (neutral compound)


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Whythishappens (Samecompound in onereactiontake as refEntity CHEBI ID from RHEA and in other CHEBI ID from ECOCYC, whichiswrong in several cases)???

Whatshouldwe do in this case?? Normallychangethewrong CHEBI xreference, buthow, manuallyoritcouldbepossibleanautomaticsolution??


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

  • Additionalproblem: BIGG crossreferences are notreportedfor:

    • BIGG reversible reactions VS ECOCYC reversible reactions: Same RHEA xreference in iAF1260-ECOCYC in RHEA. i.e.:iAF1260:ASAD

Bidireactional ECOCYC rxnsdecomposed in twodirectedreactions in Microme; xrefto RHEA and ECOCYC; notto BIGG:ASAD


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

Additionalproblem:Pathwayswithconnectivityproblems in thedatabaseversionpresented in thejamboree (microme_prerelease_eco_meta_cyc_14_5_iaf1260) differs in thecurrentdatabase (microme_prerelease_ecocyc_15_0_iaf1260).

i.e.: GDP-mannosebiosynthesis, wherethetwoinitialreactionsappearedunconnected in theinitialdatabaseduetodifferent CHEBI ID forfructose 6P in RHEA reactionsbut in thecurrentversionthereis no connectivityproblem:

RHEA comp

RefEntityMicrome

Chebixref ECOCYC

CHEBI:57584

CHEBI:17719

CHEBI:17719

Wrongxref ECOCYC (neutral comp; notmajormicrospph 7.3)

Connectivityproblem

iAF1260:PGI; RHEA:11819

CHEBI:57579 (RHEA:11819); racemic+linear

CHEBI:57634 (RHEA:12359); beta+cyclic

CHEBI:57634

CHEBI:57634

iAF1260:MAN6PI RHEA:12359

CHEBI:58735

CHEBI:58735

CHEBI:60332

iAF1260:PMAMNRHEA:12359

CHEBI:58409

CHEBI:58409

CHEBI:58049

iAF1260:MAN1PT2 RHEA:12906

CHEBI:57527

No Chebixref

CHEBI:57527


In blue isolated reactions in the reactome pathway reproduces the situation in ecocyc

  • Additionalproblem:Pathwayswithconnectivityproblems in thedatabaseversionpresented in thejamboree (microme_prerelease_eco_meta_cyc_14_5_iaf1260) differs in thecurrentdatabase (microme_prerelease_ecocyc_15_0_iaf1260).

  • i.e.: GDP-mannosebiosynthesis, wherethetwoinitialreactionsappearedunconnected in theinitialdatabaseduetodifferent CHEBI ID forfructose 6P in RHEA reactionsbut in thecurrentversionthereis no connectivityproblem:

    • WhichisthecriteriausedtoassignreferenceEntityID´stomicromecompounds (some times PubChemcompounds, CHEBI compoundsfrom ECOCYC, CHEBI compoundsfrom RHEA, KEGG compounds in some cases)

    • Whatshouldwe do in these cases of connectivityproblems in RHEA reactionsliketheone of GDP-mannosebiosynthesis:

      • Edit RHEA reactiontosolvetheproblem of connectivity, i.e.changing CHEBI:57579 by CHEBI:57634 in RHEA:11819. Problem: Itsupposetoedit IUBMB reactions (RHEA reactionsassociatedto IUBMB EC numbers)

      • Create novel reactionequivalentto RHEA:11819 butwith CHEBI:57634 (beta isoformfructose 6P, cyclic) instead CHEBI:57579 (racemicfructose 6P, linear). Problem: ECOCYC xreferencesfrom RHEA:11819 (IUBMBrxnassociatedto EC:5.1.3.9) shouldbealso removed from RHEA:11819 and changedto novel RHEA reaction


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