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Chunk #64 — Method Details — Functional enrichment analysis of landmark gene content

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A Next Generation Connectivity Map: L1000 Platform and the First 1,000,000 Profiles.
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For every landmark gene we accessed from NCBI entrez its current gene description and family assignment. We also annotated every landmark gene with the pathway (as defined in MSigDB) in which it is thought to function (when available). Finally, we looked up its biological/molecular category from Gene Ontology (GO). These annotations were analyzed for functional enrichment to ask if the landmarks, when considered as a set, are dominated by a few functions or if on the whole they map to many different functions. For example, at one extreme the transcriptionally active genes could belong to basic regulatory processes (e.g transcription factors).