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Table 1 Comparison of microarray databases (and associated tools) in public domain

From: The PhenoGen Informatics website: tools for analyses of complex traits

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

  1. 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).
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