Table 1.
Public repositories for S. cerevisiae
|
Saccharomyces cerevisiae Databases | |||||||||
|---|---|---|---|---|---|---|---|---|---|
| Database | Protein interaction | Biochemical pathway | Network dataset | Expression dataset | Metabolomics data (metabolite/reaction) | Year of publication | Lastest update | Accessibility | Reference |
| Biogrid | 342 878 | – | – | – | – | 2006 | 2015 | Download/Query | [33] |
| DIP | 24 618 | – | – | – | – | 2002 | 2014 | Download | [34] |
| MINT | 62 621 | – | – | – | – | 2002 | 2012 | Download | [35] |
| SGD | 340 493 | 187 | – | 339 | – | 1998 | 2015 | Download/Query | [32] |
| YeastNet V3 | 362 421 | – | 72 | – | – | 2004 | 2013 | Download | [36] |
| Yeast Interactome Database | – | – | 6 | – | – | 2008 | 2008 | Download/Query | [37] |
| MetaCyc | – | 268 | – | – | – | 2001 | 2015 | Download/Query | [38] |
| KEGG | – | 109 | – | – | – | 1999 | 2015 | Download/Query | [2] |
| ExpressDB | – | – | – | 46 | – | 2000 | 2006 | Download | [39] |
| yStrex | – | – | – | 82 | – | 2013 | 2014 | Download/Query | [40] |
| YMDB | – | – | – | – | 2027/916 | 2012 | 2012 | Download/Query | [41] |
| BIGG | – | – | – | – | iMM904: 1226/1557 | 2010 | 2015 | Query | [42] |
| iND750: 1056/1266 | |||||||||
Note. Twelve widely used databases are listed and the statistics of data in each database are presented. For example, SGD database provides 340 493 interaction records for yeast protein pairs from different types of experiments and 187 biochemical pathways for S. cerevisiae. SGD also provides 339 expression datasets from experiments. Besides the statistics, the website and related reference are also presented.