Table 1.
Comparison of microarray databases (and associated tools) in public domain
| Functionality | Array Express | GEO | GeneNetwork/WebQTL | Stanford Microarray database | BASE | PhenoGen |
| Data warehouse (MIAME compliant) | Yes | Yes | No | Yes | Yes | Yes |
| Microarray platform support | ||||||
| Oligonucleotide | Yes | Yes | Yes | Yes | No | Yes |
| cDNA | Yes | Yes | Yes | Yes | Yes | Yes |
| Microarray data search | ||||||
| Gene based | Yes | Yes | Yes | Yes | Yes | No |
| Hybridization (array) based | Yes | Yes | No | Yes | Yes | Yes |
| Expt based | Yes | Yes | Yes | Yes | Yes | Yes |
| Sample attributes | Yes | Yes | No | Yes | Yes | Yes |
| Microarray data retrieval | ||||||
| Gene based | Yes | Yes | Yes | Yes | Yes | Yes |
| Hybridization (array) based | Yes | Yes | No | Yes | Yes | Yes |
| Expt based | Yes | Yes | No | Yes | Yes | Yes |
| Microarray data analysis | ||||||
| QC | No | No | No | Yes | No | Yes |
| Normalization | Yes | No | Yes | Yes | Yes | Yes |
| Filtering | Yes | No | No | Yes | Yes | Yes |
| "in-silico analysis" | ||||||
| Data sharing | Yes | No | ? | Yes | Yes | Yes |
| "in-silico experiments" | Yes | No | No | ? | ? | Yes |
| Statistics | "Different options" | "Plug-Ins" | ||||
| Basic stats | Yes | No | Yes | Yes | ? | Yes |
| ANOVA | Yes | No | No | Yes | ? | Yes |
| Clustering | Yes | No | Yes | Yes | ? | No |
| Correlation | No | No | Yes | No | ? | Yes |
| Gene lists | ||||||
| Annotations (Dynamic) | No | No | Yes | Yes | No | Yes |
| Comparisons | No | No | Yes | ? | No | Yes |
| eQTL | No | No | Yes | No | No | Yes |
| pQTL – Gene location overlapp | No | No | No | No | No | Yes |
| pQTL – eQTL overlapp | No | No | No | No | No | Yes |
| Promoter analysis | No | No | No | No | No | Yes |
| Literature search | No | No | No | No | No | Yes |
| System requirements | ||||||
| Local | Yes | No | No | Yes | Yes | No |
| Web-based | Yes | Yes | Yes | Yes | Yes | Yes |
| LIMS | ||||||
| Built-in | Yes | No | No | Yes | Yes | No |
| Programming expertise needed | ||||||
| Expert | Yes | Yes | ||||
| Novice | Yes | Yes | Yes | |||
| None | Yes | Yes | Yes | |||
| Functionality index (Yes/No ratio) | 2.333 | 0.666 | 0.933 | 3.83 | 1.888 | 6.500 |
This table describes various microarray databases. The majority of the functions listed are described in detail in Additional file 2 (PhenoGen user manual). "System requirements" indicates whether there are special computational requirements to use the database and associated tools; "LIMS" (Laboratory Information Management System) indicates whether LIMS is available; and "Programming expertise needed" is self-explanatory. Functionality index is a ratio of the number of "Yeses" to "Nos" for a given database. "?" indicates that the functionality of the database was not readily evident ("?" were not used to determine functionality index).