Table 1.
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).