BMC Genomics 2007, 8:117 http://www.biomedcentral.com/1471-2164/8/117 Additional file 4 JNK cascade is a well modeled pathway of cervical cancer by most cell lines whereas the RNA processing pathway is poorly modeled by most cell lines. A detailed view of two specific pathways indicate some pathways are well represented by many cell lines ("JNK Cascade"; GO:7254), whereas other pathways ("RNA Processing"; GO:6396) are poorly modeled by many cell lines. Missing data indicates significance was not reached for a particular cell line and not a correlation of -0.4. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-117-S4.pdf] Additional file 5 Presentation of the day of hybridization, microarray print batch (written "HS-print batch-slide number"), and dendrogram. In order to reduce the chance of non-biological artifacts that may result in high correlations between samples, replicates for the most part were hybridized on different days. In addition, many samples, including tissue biopsies, were run on different print sets and different days. Additional file 3 presents the day of hybridization, print set, and dendrogram. Clusters on the dendrogram span print sets and days of hybridization, indicating high correlations observed in the analysis result from biological similarity and not technical artifacts. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-117-S5.xls] Additional file 6 Percent of SVD component variance. The first 3 components plotted in Figure 2B account for approximately 40% of the variance. SVD was cal- culated using Matlab. Click here for file [http://www.biomedcentral.com/content/supplementary/1471- 2164-8-117-S6.pdf] Acknowledgements This research was supported by The University of Texas Center for Bio- medical Engineering and grants from the NIH, NSF, Welch (F1515), and Packard Foundations (E.M.M.). 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