A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
Citations
9 citations
9 citations
Cites methods from "A Next Generation Connectivity Map:..."
...In the comparison between the enhanced COXEN gene selection and random genes picked from the LINCS gene set [22], again, models built using the enhanced COXEN method always statistically significantly outperformed models built using randomly picked genes (adjusted p-values ≤ 0....
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...We compared the prediction performance of models built based on genes selected by the enhanced COXEN method to those of prediction models built based on three baseline gene selection methods, including genes randomly selected from all available genes, genes randomly selected from the LINCS gene set that includes 942 “landmark” genes that well represent cellular transcriptomic changes identified in the Library of Integrated Network-Based Cellular Signatures (LINCS) project [22], and genes selected by the original COXEN method that was applied ignoring the drug difference....
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9 citations
9 citations
9 citations
Cites background from "A Next Generation Connectivity Map:..."
...Lists of Differentially Expressed Genes (DEGs) per topography were queried in the Connectivity Map (CMap) (Subramanian et al., 2017), a library of gene expression signatures induced by chemical compounds or genetic interference (perturbants), and connectivity scores between the topography-induced DEGs and Connectivity Map DEGs were retrieved....
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...Lists of Differentially Expressed Genes (DEGs) per topography were queried in the Connectivity Map (CMap) (Subramanian et al., 2017), a library of gene expression signatures induced by chemical compounds or genetic interference (perturbants), and connectivity scores between the topography-induced…...
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...The gene signatures related to cell shape and their underlying topographies can be used to browse the Connectivity Map database for genetic signatures that resemble the effect of small molecule or RNAi-induced gene signatures (Subramanian et al., 2017)....
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