Name
Abstract | ||
|---|---|---|
Background To date, several genome-scale network reconstructions have been used to describe the metabolism of the yeast Saccharomyces cerevisiae, each differing in scope and content. The recent community-driven reconstruction, while rigorously evidenced and well annotated,
under-represented metabolite transport, lipid metabolism and other pathways, and was not amenable to constraint-based analyses
because of lack of pathway connectivity.
Results We have expanded the yeast network reconstruction to incorporate many new reactions from the literature and represented these
in a well-annotated and standards-compliant manner. The new reconstruction comprises 1102 unique metabolic reactions involving
924 unique metabolites - significantly larger in scope than any previous reconstruction. The representation of lipid metabolism
in particular has improved, with 234 out of 268 enzymes linked to lipid metabolism now present in at least one reaction. Connectivity
is emphatically improved, with more than 90% of metabolites now reachable from the growth medium constituents. The present
updates allow constraint-based analyses to be performed; viability predictions of single knockouts are comparable to results
from in vivo experiments and to those of previous reconstructions.
Conclusions We report the development of the most complete reconstruction of yeast metabolism to date that is based upon reliable literature
evidence and richly annotated according to MIRIAM standards. The reconstruction is available in the Systems Biology Markup
Language (SBML) and via a publicly accessible database http://www.comp-sys-bio.org/yeastnet/. |
Year | DOI | Venue |
|---|---|---|
2010 | 10.1186/1752-0509-4-145 | BMC systems biology |
Keywords | Field | DocType |
systems biology,lipid metabolism,bioinformatics,algorithms,metabolomics | Genome,Lipid metabolism,Computer science,Metabolomics,Systems biology,Yeast,Saccharomyces cerevisiae,Bioinformatics,SBML,Flux balance analysis | Journal |
Volume | Issue | ISSN |
4 | 1 | 1752-0509 |
Citations | PageRank | References |
28 | 1.35 | 11 |
Authors | ||
19 | ||
Name | Order | Citations | PageRank |
|---|---|---|---|
| Paul D. Dobson | 1 | 28 | 1.35 |
| Kieran Smallbone | 2 | 142 | 9.16 |
| Daniel Jameson | 3 | 386 | 26.54 |
| Evangelos Simeonidis | 4 | 93 | 4.73 |
| Karin Lanthaler | 5 | 28 | 1.35 |
| Pinar Pir | 6 | 42 | 2.92 |
| Chuan Lu | 7 | 28 | 1.35 |
| Neil Swainston | 8 | 274 | 14.07 |
| Warwick Dunn | 9 | 74 | 5.38 |
| Paul Fisher | 10 | 272 | 11.71 |
| Duncan Hull | 11 | 1008 | 67.40 |
| Marie Brown | 12 | 35 | 2.34 |
| Olusegun Oshota | 13 | 28 | 1.35 |
| Natalie J. Stanford | 14 | 45 | 3.32 |
| Douglas B Kell | 15 | 1004 | 94.11 |
| Ross D. King | 16 | 1774 | 194.85 |
| Stephen G. Oliver | 17 | 333 | 24.18 |
| Robert Stevens | 18 | 5538 | 499.01 |
| Pedro Mendes | 19 | 349 | 53.14 |