Several sample files are provided under Expander/sample_input_files/. These files include:
expressionData1.txt – A gene expression data file that was generated using the cDNA microarray technology. This is a partial dataset extracted from a yeast cell cycle dataset generated by Spellman et al 1998 (see the References section). Gene identifiers in this set are yeast ORFs, which are the same identifiers used in the annotation and TF fingerprint files that are supplied with Expander. Thus, no conversion file is required.
ExpressionData2.txt – A gene expression data file that was generated in the Affymetrix technology. This dataset was generated in an experiment that was conducted in out laboratory on human cells, and has not yet been published. Affymetrix chips of type HG-Focus were used for this experiment and thus, the HG-Focus conversion file is required for the analysis (can be downloaded from the download page).
ExpressionData3.txt – taken from Murray JI, Whitfield ML, Trinklein ND, Myers RM, Brown PO, Botstein D: Diverse and specific gene expression responses to stresses in cultured human cells. Mol Biol Cell 2004, 15:2361-2374. A corresponding conversion file (from clone-Ids to LL-Ids) is available at the same directory under the name Data3Conversion.txt.
expressionWithDetection.txt – A gene expression data file with detection calls, that was generated in the Affymetrix technology. This dataset was generated in an experiment that was conducted in our laboratory on human cells. Affymetrix GeneChip HGU133 Plus 2.0 arrays were used for this experiment.
expressionData1Clustering.sol – A clustering solution that was generated by Expander for the dataset in ‘expressionData1.txt’.
geneSetsData1.txt – Contains sets of human genes (in Entrez/Locus-Link Ids).
Data3Conversion.txt - A conversion file for expressionData3.txt.