Difference between revisions of "Main Page"

From metabolic_network
Jump to navigation Jump to search
(Created page with "Category:reaction == Reaction RXN-1404 == * direction: ** left-to-right * ec-number: ** [http://enzyme.expasy.org/EC/3.5.5.1 ec-3.5.5.1] == Reaction formula == * 1 INDOL...")
(Created page with "== ESILGEM description == ''Ectocarpus siliculosus'' is a model filamentous brown alga. It was the first brown alga to be sequenced ([doi:10.1038/nature09016 Cock et al., Na...")
 
(4 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
[[Category:reaction]]
+
== ESILGEM description ==
−
== Reaction RXN-1404 ==
+
 
−
* direction:
+
''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).  
−
** left-to-right
+
 
−
* ec-number:
+
 
−
** [http://enzyme.expasy.org/EC/3.5.5.1 ec-3.5.5.1]
+
== Automatic reconstruction with [http://aureme.genouest.org AuReMe] ==
−
== Reaction formula ==
+
Model summary: [[MEDIA:summary.txt|summary]]
−
* 1 [[INDOLEYL-CPD]][c] '''+''' 2 [[WATER]][c] '''=>''' 1 [[AMMONIUM]][c] '''+''' 1 [[INDOLE_ACETATE_AUXIN]][c]
+
 
−
== Gene(s) associated with this reaction  ==
+
Download '''AuReMe''' Input/Output [LINK OR MEDIA data]
−
* Gene: [[Ec-01_002370]]
+
 
−
** Category: [[orthology]]
+
The automatic reconstruction of ''Ectocarpus siliculosus'' results to a Genome scale [[MEDIA:model.xml|Model]] containing 1987 reactions, 2140 metabolites, 2288 genes and 1103 pathways. This GeM was obtained based on the following sources:
−
*** Source: [[output_pantograph_aragem]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
+
* Based on annotation data:
−
* Gene: [[Ec-26_000350]]
+
** Tool: [http://bioinformatics.ai.sri.com/ptools/ PathwayTools]
−
** Category: [[orthology]]
+
** Creation of a metabolic network containing 1661 reactions
−
*** Source: [[output_pantograph_aragem]], Tool: [[pantograph]], Assignment: n.a, Comment: n.a
+
* Based on orthology data:
−
== Pathway(s)  ==
+
** Tool: [http://pathtastic.gforge.inria.fr Pantograph]
−
* [[PWYQT-4476]], indole glucosinolate activation (herbivore attack):
+
** Creation of a global metabolic network containing 440 reactions
−
** '''1''' reactions found over '''13''' reactions in the full pathway
+
*** From template ''aragem'' creation of a metabolic network containing: 440 reactions
−
* [[PWY-5026]], indole-3-acetate biosynthesis V (bacteria and fungi):
+
* Based on gap-filling:
−
** '''1''' reactions found over '''1''' reactions in the full pathway
+
** Tool: [https://pypi.python.org/pypi/meneco Meneco]
−
* [[PWY-581]], indole-3-acetate biosynthesis II:
+
*** 85 reaction(s) added
−
** '''2''' reactions found over '''12''' reactions in the full pathway
+
* Based on expertise:
−
== Reconstruction information  ==
+
** 80 reaction(s) added
−
* category: [[orthology]]; source: [[output_pantograph_aragem]]; tool: [[pantograph]]; comment: n.a
+
 
−
== External links  ==
+
[[FILE:venn.png|frameless|border]]
−
* RHEA:
+
 
−
** [http://www.ebi.ac.uk/rhea/reaction.xhtml?id=45777 45777]
+
 
−
* LIGAND-RXN:
+
== Collaborative curation ==  
−
** [http://www.genome.jp/dbget-bin/www_bget?R03093 R03093]
+
* Suggest reactions to add or remove:
−
{{#set: direction=left-to-right}}
+
** Download this [[MEDIA:Add_delete_reaction.csv|form]]
−
{{#set: ec-number=ec-3.5.5.1}}
+
* Suggest new reactions to create and add:
−
{{#set: nb gene associated=2}}
+
** Download this [[MEDIA:Reaction_creator.csv|form]]
−
{{#set: nb pathway associated=3}}
+
* '''Follow the examples given in the form(s) to correctly share your suggestions'''
−
{{#set: reconstruction category=orthology}}
+
* Send the filled form(s) to: gem-aureme[at]inria.fr
−
{{#set: reconstruction tool=pantograph}}
 
−
{{#set: reconstruction comment=n.a}}
 
−
{{#set: reconstruction source=output_pantograph_aragem}}
 

Latest revision as of 09:01, 18 March 2021

ESILGEM description

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 (Cormier et al., New Phytol 2017 was published in 2018 (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).


Automatic reconstruction with AuReMe

Model summary: summary

Download AuReMe Input/Output [LINK OR MEDIA data]

The automatic reconstruction of Ectocarpus siliculosus results to a Genome scale Model containing 1987 reactions, 2140 metabolites, 2288 genes and 1103 pathways. This GeM was obtained based on the following sources:

  • Based on annotation data:
    • Tool: PathwayTools
    • Creation of a metabolic network containing 1661 reactions
  • Based on orthology data:
    • Tool: Pantograph
    • Creation of a global metabolic network containing 440 reactions
      • From template aragem creation of a metabolic network containing: 440 reactions
  • Based on gap-filling:
    • Tool: Meneco
      • 85 reaction(s) added
  • Based on expertise:
    • 80 reaction(s) added

Venn.png


Collaborative curation

  • Suggest reactions to add or remove:
  • Suggest new reactions to create and add:
  • Follow the examples given in the form(s) to correctly share your suggestions
  • Send the filled form(s) to: gem-aureme[at]inria.fr
Retrieved from "http://gem-aureme.genouest.org//esilgem/index.php?title=Main_Page&oldid=88554"