Fig. 1

Deriving pathway-response signatures for 11 pathways. a Reasoning about pathway activation. Most pathway approaches make use of either the set (top panel) or infer or incorporate structure (middle panel) of signaling molecules to make statements about a possible activation, while signature-based approaches such as PROGENy consider the genes affected by perturbing the pathway. b Workflow of the data curation and model building. (1) Finding and curation of 208 publicly available experiment series in the ArrayExpress database, (2) Extracting 556 perturbation experiments from series’ raw data, (3) Performing QC metrics and discarding failures, (4) Computing z-scores per experiment, (5) Using a linear regression model to fit genes responsive to all pathways simultaneously obtaining the z-coefficients matrix, (6) Assigning pathway scores using the coefficients matrix and basal expression data. See methods section for details. c Size of the data set compared to an individual gene expression signature experiment. The amount of experiments that comprise each pathway is shown to scale and indicated. Figure 1b (2) created by Guillaime Paumier is published under a CC-BY-SA license, sourced from https://commons.wikimedia.org/wiki/File:DNA_microarray.svg. Figure 1b (4) is an adaptation (by Chen-Pan Liao) of the original work of User:Jhguch at en.wikipedia, published under a CC-BY-SA license, sourced from https://commons.wikimedia.org/wiki/File:Boxplot_vs_PDF.svg. Figure 1b (6) is an adaptation (by User:Ogrebot) of the original work of User:Bilou at en.wikipedia, published under a CC-BY-SA license, sourced from https://commons.wikimedia.org/wiki/File:Matrix_multiplication_diagram_2.svg