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Open Access Research article

Predicting environmental chemical factors associated with disease-related gene expression data

Chirag J Patel123 and Atul J Butte123*

Author Affiliations

1 Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA

2 Center for Biomedical Informatics Research, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA

3 Lucile Packard Children's Hospital, 725 Welch Road, Palo Alto, CA 94304, USA

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BMC Medical Genomics 2010, 3:17  doi:10.1186/1755-8794-3-17

Published: 6 May 2010

Additional files

Additional file 1:

Differential gene expression summary information for the verification and query stage and additional lung and breast cancer queries. Additional file 1 contains information regarding the Significance Analysis of Microarray (SAM) procedure for the verification and query stage, specifically the types of samples analyzed, the median false discovery rate for the analysis, and the number of differentially expressed genes found. Information for the verification stage is in Supplementary Table S1, for the query stage in Supplementary Table S2. We also conducted additional query predictions on gene expression datasets related to the ones described in the main manuscript, specifically on lung cancer smoker samples and tumorigenic breast cancer cell lines. These data are analogous to the Tables 2, 3, 4 in the main manuscript and are seen in Supplementary Tables S3, S4, and S5. Figures analogous to Figure 4 are also seen in Supplementary Figures S1 and S2.

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