The Silverman Lab
University of Massachusetts Medical School
Division of Infectious Disease, Department of Medicine

Microarray Data from Silverman et al., 2003

This is the web supplement to Silverman et al. JBC 2003. The site includes all analyzed, normalized, and raw data from a series of 27 cDNA microarray hybridization presented in the paper. Our arrays were printed at the Bauer Center for Genomics Research at Harvard University. These arrays include the Drosophila Gene Collection, version 1.0 (DGC 1.0), from the Berkeley Drosophila Genome Project. Also, a number of control genes were printed in multiple locations throughout the array.

Statistical analysis was performed with BAGEL, a software package for the Bayesian analysis of gene expression levels. For more information on BAGEL, see the BAGEL paper from Genome Biology by Jeff Townsend and Dan Hartl, or to download the software visit the web site of Jeff Townsend.

The BAGEL analyzed data is presented in one tab-delimited text file. This data includes the relative expression level of each gene in each condition and a statistical analysis of its 95% confidence interval. BAGEL analyzed data

The normalized data includes one tab-delimited text file that include the data from all hybridizations. Normalization was performed as described in the paper. Because the background signal was different for Taq and Herculase amplified cDNA spots, the normalization was performed independently for each type of spot. normalized data

The raw data files include the entire output from the GenePix scanner. One tab-delimited text file is available for each hybridization.

Hybridization

Cy3
(stimulation/RNAi)
Cy5
(stimulation/RNAi)
 
0.1wt  none/none LPS/none click here to download
0.1ikk-beta none/IKKbeta LPS/IKKbeta click here to download
0.1tak none/TAK LPS/TAK1 click here to download
0.1hep      none/hep LPS/hep  click here to download
0.1bsk  none/bsk LPS/bsk click here to download
1.1wt none/none LPS/none click here to download
1.1lacZ none/lacZ LPS/lacZ click here to download
1.1ikk-gamma none/IKKgamma LPS/IKKgamma click here to download
1.1tak none/TAK LPS/TAK click here to download
1.1hep none/hep LPS/hep click here to download
1.1bsk none/bsk LPS/bsk click here to download
1.2hep LPS/none LPS/hep click here to download
1.2bsk LPS/none LPS/bsk click here to download
1.2ikk-gamma LPS/none LPS/IKKgamma click here to download
1.2tak LPS/none LPS/TAK1 click here to download
2.1hep  LPS/hep LPS/none click here to download
2.1bsk  LPS/bsk LPS/none click here to download
2.1ikk-gamma  LPS/IKKgamma LPS/none click here to download
2.1tak  LPS/TAK1 LPS/none click here to download
3.1hep  LPS/hep LPS/none click here to download
3.1bsk  LPS/bsk LPS/none click here to download
3.1ikk-gamma  LPS/IKKgamma LPS/none click here to download
3.1tak  LPS/TAK1 LPS/none click here to download
3.2hep  LPS/none LPS/hep click here to download
3.2bsk LPS/none LPS/bsk click here to download
3.2ikk-gamma LPS/none LPS/IKKgamma click here to download
3.2tak        LPS/none LPS/TAK1 click here to download