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| − | == ESILGEM description ==
| + | {{#ask: [[Category:reaction]] [[reconstruction category::orthology]] |
| − | | + | | ?common-name |
| − | ''Ectocarpus siliculosus'' is a model filamentous brown alga. It was the first brown alga to be sequenced ([doi:10.1038/nature09016 Cock et al., Nature 2010]), and the genome sequence was used to build the first brown algal genome-scale metabolic network ([doi:10.1111/tpj.12627 Prigent et al., The Plant Journal, 2014]), using a preliminary version of the AuReMe pipeline. A second version of the genome-scale metabolic network, based on an improved version of the genome assembly and annotation ([https://doi.org/10.1111/nph.14321, Cormier et al., New Phytol 2017 ] was published in 2018 ([https://doi.org/10.1371/journal.pcbi.1006146 Aite et al., Plos Comp. Biol]). Now, in a more focussed follow-up study (Girard et al., ''in preparation''), we are curating specifically the sterol biosynthesis pathways (PWY-8191, PWY-8238).
| + | | ?ec-number |
| − | | + | | ?reconstruction tool |
| − | | + | | ?reconstruction source |
| − | == Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
| + | | ?reconstruction comment |
| − | Model summary: [[MEDIA:summary.txt|summary]]
| + | | ?nb gene associated |
| − | | + | | ?nb pathway associated |
| − | Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
| + | }} |
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| − | The automatic reconstruction of ''Ectocarpus siliculosus'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1992 reactions, 2146 metabolites, 2290 genes and 1103 pathways. This GeM was obtained based on the following sources:
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| − | * Based on annotation data:
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| − | ** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
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| − | ** Creation of a metabolic network containing 1661 reactions
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| − | * Based on orthology data:
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| − | ** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
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| − | ** Creation of a global metabolic network containing 440 reactions
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| − | *** From template ''aragem'' creation of a metabolic network containing: 440 reactions
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| − | * Based on gap-filling:
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| − | ** Tool: [https://pypi.python.org/pypi/meneco Meneco]
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| − | *** 85 reaction(s) added
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| − | * Based on expertise:
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| − | ** 80 reaction(s) added
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| − | [[FILE:venn.png|frameless|border]]
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| − | == Collaborative curation ==
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| − | * Suggest reactions to add or remove:
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| − | ** Download this [[MEDIA:Add_delete_reaction.csv|form]]
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| − | * Suggest new reactions to create and add:
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| − | ** Download this [[MEDIA:Reaction_creator.csv|form]]
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| − | * '''Follow the examples given in the form(s) to correctly share your suggestions'''
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| − | * Send the filled form(s) to: gem-aureme@inria.fr
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