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Open Access Highly Accessed Research article

The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions

Ottar Rolfsson1, Bernhard Ø Palsson1 and Ines Thiele12*

Author Affiliations

1 Center for Systems Biology, University of Iceland, Sturlugata 8, 101 Reykjavik, Iceland

2 Faculty of Industrial Engineering, Mechanical Engineering & Computer Science, University of Iceland, 101 Reykjavik, Iceland

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BMC Systems Biology 2011, 5:155  doi:10.1186/1752-0509-5-155

Published: 1 October 2011

Additional files

Additional file 1:

Metabolic subsystem distribution of the 175 blocked reactions. The distribution of the blocked reactions identified in RECON 1 within metabolic subsystems.

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Additional file 2:

Dead-end metabolites can cause multiple blocked reactions. In the majority of cases, dead-end metabolites only cause one blocked reaction. When a dead-end metabolite is at the end or beginning of a reaction cascade however, it inhibits flux through all reactions, which are part of the reaction cascade. The figure shows the number of blocked reactions found in the reaction cascades. For example, there is one reaction cascade, which has 14 blocked reactions.

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Additional file 3:

The SMILEY solution distribution is not dependent upon the metabolic pathway. Blocked reactions can have multiple SMILEY solutions independent of the metabolic pathway, of which the blocked reaction is a part.

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Additional file 4:

Characterisation of alternative SMILEY solution. The figure shows the solution categories of the alternative SMILEY solutions to blocked reactions, which had a category I (A), category II (B) or a category III (C) S1 solution. A) 30% of the blocked reactions with a category I S1 solution had alternative category III solutions. The remaining 70% had either an alternative category I solution or none at all. B) 61% of the blocked reactions, which had category II S1 solution, had alternative category II or III solutions. C) None of the blocked reactions, which had category, III S1 solutions had alternative category solutions as expected.

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Additional file 5:

The pathway distribution of blocked reactions and their SMILEY S1 solutions categories. The figure shows the SMILEY S1 solution category as a percentage of the total number of blocked reactions found within a particular metabolic pathway. The number of blocked reactions within each metabolic pathway and their SMILEY solution type is also shown. Some blocked reactions, such as those involved in amino acid metabolism, are easily bypassed using functionalities already described in the KEGG, represented by category I and II SMILEY solutions. Others, such as those involved in glycan biosynthesis, can only be solved by transport of their causative dead-end metabolite out of the system.

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Additional file 6:

The filtered S1 SMILEY output. The table contains the filtered SMILEY S1 output as described in materials and methods. The identified blocked reaction is given in column A. Columns B-J report properties of the blocked reactions i.e., causative dead end metabolites, BiGG confidence scores, cellular compartment, whether or not the blocked reaction is in a cascade, blocked reaction components, associated genes, the metabolic subsystem and the metabolic pathway the blocked reaction occurs in. Columns K-O report properties of the S1 solution i.e. the solution category, the experimentally reported directionality and computed directionalities of blocked reactions having category I reversal solutions, the number of resolving reactions composing the solution and the KEGG identifiers of each resolving reaction. The remaining columns report properties of each individual resolving reaction comprising the SMILEY solution i.e. KEGG identifiers, resolving reaction components, metabolic pathway and subsystem and any associated enzyme commission numbers or known human genes.

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Additional file 7:

The complete SMILEY output. The table contains the complete SMILEY output with up to twenty solutions for each identified blocked reaction. The identified blocked reaction is given in column A. In columns B-D the properties of the blocked reaction are reported (reaction components, gene and metabolic subsystem). In column E the resolving reactions comprising the complete SMILEY solution for the blocked reaction is reported with KEGG reaction identifiers. In the following columns the properties of the resolving reactions are reported (reaction components, reaction subsystem, enzyme commission number and gene).

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