A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
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Cites methods from "A Next Generation Connectivity Map:..."
...To test this hypothesis, we leveraged the CMAP database to ask whether large-scale gene perturbations have opposing effects on the trajectories of these two modules (Subramanian et al., 2017)....
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...This signature was used to query 7,494 gene overexpression or knockdown experiments carried out across 9 cell lines for similar (positive connectivity score) or opposite (negative connectivity score) effects on gene expression signatures, incorporating Kolmogorov-Smirnov statistics (a nonparametric, rank-based pattern-matching strategy) as described (Lamb et al., 2006; Subramanian et al., 2017)....
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...06 (de Leeuw et al., 2015) https://ctg.cncr.nl/software/magma Broad’s CMAP database, version CLUE (Subramanian et al., 2017) (https://clue.io) CQN Package v 1.18.0 (Hansen et al., 2012) Source (“http://bioconductor.org/biocLite.R”) STRING for PPI (Szklarczyk et al., 2017) https://string-db.org GOElite Package (Zambon et al., 2012) http://www.genmapp.org/go_elite/ Cytoscape v3....
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...Connectivity Map (CMAP) Analysis—For a given module, the top 150 module genes (ranked by kME) were used as input for the QUERY app in the Broad’s CMAP database, version CLUE (Subramanian et al., 2017)....
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...For a given module, the top 150 module genes (ranked by kME) were used as input for the QUERY app in the Broad’s CMAP database, version CLUE (Subramanian et al., 2017)....
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