The M3D (Many Microbes Microarray) Database is a free resource for viewing, analyzing and downloading Affymetrix expression profiles compendia for several organisms including E. coli, S. oneidensis & S. cerevisiae. All profiles for an organism are normalized to enable maximum inter-chip compatibility.

References
JJ Faith, et al. (2007) PLoS Biology [html]



The CLR algorithm (Context Likelihood of Relatedness) infers regulatory interactions between transcription factors and their targets using a compendium of gene expression profiles.

References
JJ Faith, et al. (2007) PLoS Biology [html]

Download
The CLR algorithm may be downloaded and used freely for non-profit use. Commercial users please contact Tim Gardner.

  
 
 

The MNI algorithm predicts the mechanism of action (gene targets) of drug compounds or other stimuli using a compendium of gene expression profiles.

References
D di Bernardo, et al. (2005) Nature Biotechnology [pdf]
H Xing, et al. (2006) Nature Protocols [pdf]

 Download
The MNI algorithm may be downloaded and used freely for non-profit use. Commercial users please contact Tim Gardner.


We have developed several additional algorithms for network inference, as described in our PLoS Biology 2007 publications. These include regression networks, Bayes networks and derivatives of the ARACNE algorithm.

References
JJ Faith, et al. (2007) PLoS Biology [html]

Download
These algorithms are available for download at the supplemental website for Faith et al., PLoS Biology, 2007.

  
Update
We will release an enhanced and more robust algorithm for predicting drug MOA in 2007. Please check back for this update.

Also visit our public wiki containing additional protocols, resources, tools, and documents.