Data from: Significance Analysis of Prognostic Signatures

 

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Title Breast Cancer Data
Downloaded 255 times
Description Breast cancer data. This R-workspace contains the objects: dat, dat.st, event, st, and time.
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Title Ovary_NonAngio_GSEA_Results
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Description Results from GSEA Analysis in Non-Angiogenic subtype of ovarian cancer
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Title Breast_Global_GSEA_Results
Downloaded 116 times
Description Results from GSEA Analysis in Global Breast Cancer Analysis
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Title Breast_Her2_GSEA_Results
Downloaded 111 times
Description Results from GSEA Analysis in HER2+ subtype of breast cancer
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Title Ovary_Angio_GSEA_Results
Downloaded 85 times
Description Results from GSEA Analysis in Angiogenic subtype of ovarian cancer
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Title Breast_ERHigh_GSEA_Results
Downloaded 86 times
Description Results from GSEA Analysis in ER+ high proliferation subtype of breast cancer
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Title Breast_ERNegHer2Neg_GSEA_Results
Downloaded 86 times
Description Results from GSEA Analysis in ER Neg HER2 Neg subtype of breast cancer
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Title Ovary_Global_GSEA_Results
Downloaded 87 times
Description Results from GSEA Analysis in Global ovarian cancer analysis
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Title Breast_ERLow_GSEA_Results
Downloaded 97 times
Description Results from GSEA Analysis in ER+ low proliferation subtype of breast cancer
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Title Ovarian Cancer Data
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Description Ovarian cancer data. This R-workspace contains the objects: dat, dat.st, event, st, and time.
Download README.txt (648 bytes)
Download Ovary.zip (284.3 Mb)
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Title Breast.Ps.OnPermutedData.RData
Downloaded 103 times
Description Breast.Ps.OnPermutedData.RData contains the results of performing SAPS using permuted gene sets on the breast data. P_enrich, p_pure,p_rand are each 8 x 10000 x 6 arrays with P_enrich,P_pure, and P_random p values from permuted gene sets
Download Breast.Ps.OnPermutedData.RData.zip (6.726 Mb)
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Title Ovary.Ps.OnPermutedData.RData
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Description ReadMe, Ovary.Ps.OnPermutedData.RData. Ovary.Ps.OnPermutedData.RData contains the results of performing SAPS using permuted gene sets on the ovarian data. P_enrich, p_pure,p_rand are arrays with P_enrich,P_pure, and P_random p values from permuted gene sets.
Download Ovary.Ps.OnPermutedData.RData.zip (4.084 Mb)
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Title FinalOutput_Breast
Downloaded 95 times
Description FinalOutput_Breast.RData contains the results from the subtype-specific analysis in breast cancer, including the results of the permutation-based procedure to compute p values and q values for the SAPSscores.
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Title FinalOutput_Ovary
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Description FinalOutput_Ovary.RData contains the results from the traditional scaled data set in ovarian cancer, including the results of the permutation-based procedure to compute p values and q values for the SAPSScores.
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Title molsigdb.v3.0.entrezForR.txt
Downloaded 158 times
Description molsigdb.v3.0.entrezForR contains the molsigdb, downloaded from the Broad Institute. The file is used to read the molsigdb.v3.0 gene sets into R.
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Title BreastOutput_TradScaled
Downloaded 97 times
Description BreastOutput_TradScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets.
Download BreastOutput_TradScaled.zip (883.5 Kb)
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Title BreastOutput_SubScaled
Downloaded 90 times
Description BreastOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the breast cancer meta-data set scaled by transforming each feature into its Z score across all patients within a breast cancer subtype data-set prior to merging across data-sets.
Download BreastOutput_SubScaled.zip (875.5 Kb)
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Title BreastSubtypeSpecScaleRankDir
Downloaded 87 times
Description BreastSubtypeSpecScaleRankDir contains the ranked gene lists of concordance indices used to perform the GSEA in breast cancer.
Download BreastSubtypeSpecScaleRankDir.zip (675.8 Kb)
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Title OvaryOutput_TradScaled
Downloaded 75 times
Description OvaryOutput_TradScaled.RData contains the objects: allPs, allPs.adj, sumTable.BreastOutput_TradScaled.RData. These were generated from applying the SAPS method to the ovarian cancer meta-data set scaled by transforming each feature into its Z score across all patients in a data-set prior to merging across data-sets.
Download OvaryOutput_TradScaled.zip (590.3 Kb)
Download README.txt (615 bytes)
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Title OvaryOutput_SubScaled
Downloaded 81 times
Description OvaryOutput_SubScaled.RData is an R-workspace contains the objects: allPs, allPs.adj, sumTable. These were generated from applying the SAPS method to the ovarian cancer meta-data set scaled by transforming each feature into its Z score across all patients within a ovarian cancer subtype data-set prior to merging across data-sets.
Download OvaryOutput_SubScaled.zip (574.2 Kb)
Download README.txt (576 bytes)
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Title OvaryTradScaleRankDir
Downloaded 77 times
Description OvaryTradScaleRankDircontains the ranked gene lists of concordance indices used to perform the GSEA in ovarian cancer.
Download OvaryTradScaleRankDir.zip (370.5 Kb)
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Title BreastOvary_HCv2
Downloaded 82 times
Description BreastOvary_HCv2.zip – This zip directory contains files to generate Figure 10 (Hierarchical clustering of breast and ovarian cancer subtypes based on SAPS scores) using JavaTreeView (http://jtreeview.sourceforge.net/)
Download BreastOvary_HCv2.zip (143.8 Kb)
Download README.txt (249 bytes)
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Title runSAPSonPermutedData
Downloaded 107 times
Description runSAPSonPermutedData.R – This R script generates the P_pure, P_random, and P_enrichment on random gene sets. This "biologically null" set of SAPS scores is used to compute the SAPS_q_values on the msigdb gene sets.
Download README.txt (144 bytes)
Download runSAPSonPermutedData.zip (5.377 Kb)
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Title saps
Downloaded 147 times
Description saps.R – This R script provides R commands for loading data, applying the SAPS method, and generating the SAPS p values. The script is interactive, and the user must specify the working directory, and if the analysis is on the ovarian or breast data.
Download README.txt (268 bytes)
Download saps.zip (3.91 Kb)
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Title sapsFigures
Downloaded 117 times
Description sapsFigures.R – This R script generates the figures, tables, and file used for clustering
Download sapsFigures.zip (2.054 Kb)
Download README.txt (112 bytes)
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Title computeSAPS.Permute.PValue.R
Downloaded 122 times
Description computeSAPS.Permute.PValue.R – This script generates permutation-based p and q values for the SAPSscores obtained in breast and ovarian cancer.
Download computeSAPS.Permute.PValue.R.zip (1.498 Kb)
Download README.txt (184 bytes)
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When using this data, please cite the original publication:

Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Risch T, Quackenbush J, Haibe-Kains B (2013) Significance Analysis of Prognostic Signatures. PLoS Computational Biology 9(1): e1002875. http://dx.doi.org/10.1371/journal.pcbi.1002875

Additionally, please cite the Dryad data package:

Beck AH, Knoblauch NW, Hefti MM, Kaplan J, Schnitt SJ, Culhane AC, Schroeder MS, Quackenbush J, Haibe-Kains B (2013) Data from: Significance Analysis of Prognostic Signatures. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.mk471
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