Febbo, et al., "Gene Expression Correlates of Clinical Prostate Cancer Behavior," Cancer Cell, March 2002. This document contains summary information regarding the files contained on this supplemental information website. Last updated on 3/12/02 ---------------------------------------------------------------------- Files: Prostate_TN_final0701_allmeanScale.res - Prostate normal versus tumor res file. This file contains expression values in Affymetrix's scaled average difference units (as described in the supplemental information document) for all of the prostate samples used for tumor versus normal prediction used in this study. These average difference values were generated by Affymetrix's GeneChip software. Associated with each average difference expression number is a P, M, or A label that indicates whether RNA for the gene is present, marginal, or absent, respectively (as determined by the GeneChip software) based upon the matched and mismatched probes for the genes. The file is organized such that columns contain data for samples and rows contain data for genes. Prostate_T_allmeansquare.res - Prostate tumor samples res file. This file contains expression values in Affymetrix's scaled average difference units (as described in the supplemental information document) for all of the prostate tumor samples used in this study. These average difference values were generated by Affymetrix's GeneChip software. Associated with each average difference expression number is a P, M, or A label that indicates whether RNA for the gene is present, marginal, or absent, respectively (as determined by the GeneChip software) based upon the matched and mismatched probes for the genes. The file is organized such that columns contain data for samples and rows contain data for genes. Prostate_CapPen_061901_allmeanscale.res - Prostate capsular penetration samples res file. This file contains expression values in Affymetrix's scaled average difference units (as described in the supplemental information document) for capsular penetration samples used in this study. These average difference values were generated by Affymetrix's GeneChip software. Associated with each average difference expression number is a P, M, or A label that indicates whether RNA for the gene is present, marginal, or absent, respectively (as determined by the GeneChip software) based upon the matched and mismatched probes for the genes. The file is organized such that columns contain data for samples and rows contain data for genes. Prostate_Margin_allmeanscale.res - Prostate surgical margin samples res file. This file contains expression values in Affymetrix's scaled average difference units (as described in the supplemental information document) for the prostate surgical margin samples used in this study. These average difference values were generated by Affymetrix's GeneChip software. Associated with each average difference expression number is a P, M, or A label that indicates whether RNA for the gene is present, marginal, or absent, respectively (as determined by the GeneChip software) based upon the matched and mismatched probes for the genes. The file is organized such that columns contain data for samples and rows contain data for genes. Prostate_nonrecur_vs_recur.res - Prostate tumor samples res file used for outcome prediction. This file contains expression values in Affymetrix's scaled average difference units (as described in the supplemental information document) for all of the prostate tumor samples used in this study for outcome prediction. These average difference values were generated by Affymetrix's GeneChip software. Associated with each average difference expression number is a P, M, or A label that indicates whether RNA for the gene is present, marginal, or absent, respectively (as determined by the GeneChip software) based upon the matched and mismatched probes for the genes. The file is organized such that columns contain data for samples and rows contain data for genes. prostate_normal_N01-N31.CEL.tar.gz - A 65M gzipped tar file containing 25 CEL files with raw data from the Affymetrix GeneChip software for normal prostate samples N01__normal through N31__normal. These files contain the measurements for each of the probes on the Affymetrix U95Av2 microarrays that are used to calculate the average difference values. prostate_normal_N32-N62.CEL.tar.gz - A 65M gzipped tar file containing 25 CEL files with raw data from the Affymetrix GeneChip software for normal prostate samples N32__normal through N62__normal. These files contain the measurements for each of the probes on the Affymetrix U95Av2 microarrays that are used to calculate the average difference values. prostate_tumor_T01-T30.CEL.tar.gz - A gzipped tar file containing 26 CEL files with raw data from the Affymetrix GeneChip software for tumor prostate samples T01__tumor through T30__tumor. These files contain the measurements for each of the probes on the Affymetrix U95Av2 microarrays that are used to calculate the average difference values. prostate_tumor_T31-T62.CEL.tar.gz - A gzipped tar file containing 26 CEL files with raw data from the Affymetrix GeneChip software for tumor prostate samples T31__tumor through T62__tumor. These files contain the measurements for each of the probes on the Affymetrix U95Av2 microarrays that are used to calculate the average difference values. SuppInfo_CCv3.pdf - Supplementary information document containing additional information about laboratory protocols and analytical methods. Figure1_2and3.pdf - Document containing Figures 1, 2 and 3 from the manuscript. Table1v2.pdf - Document containing Table 1 from the paper with clinical and pathological features for the dataset. Supplemental_Figure1.pdf - Supplemental figure 1 which shows a pink-o-gram of the normal and tumor samples for the top genes as defined by a nearest neighbor analysis. Supplemental_Figure2and3.pdf - Supplemental figures 2 and 3 where figure 2 shows the performance and the genes for the prediction model for the tumor vs. normal distinction and figure 3 shows the validation performance of the tumor-normal model. Supplemental_Figure4.pdf - Supplemental figure 4 shows the genes correlating with clinical and pathological features of prostate cancer. Supplemental_Figure5.pdf - Supplemental figure 5 shows the results from an independent validation of co-expressed genes correlated with Gleason score. SupplementalFigureLegendsRv1.pdf - Contains legends for the supplemental figures. ---------------------------------------------------------------------- Notes: - The raw data (CEL files) for the scans are contained in compressed archive files that have been processed by Unix commands tar and gzip. The raw data files can be extracted using WinZip on the PC (http://www.winzip.com) and StuffIt Expander on the Mac (http://www.stuffit.com/expander/).