Enhancing and Mining the Gene Expression Omnibus and DataMed with Chrome Extensions


Thu Apr 13th 10:00am to 11:00am PDT


Avi Ma'ayan


In the past two years we have developed four Chrome extensions that enhance the functionality of the Gene Expression Omnibus (GEO) and DataMed. The Chrome extensions are named: GEO2Enrichr, ARCHS4, Cite-D-Lite, and Datasets2Tools. GEO2Enrichr enables users to select control and perturbation samples from GEO dataset landing pages, and then to compute differential expression between the samples. The resultant signatures are visualized with interactive PCA and heatmaps, and piped to downstream analysis tools such as Enrichr and L1000CDS2. ARCHS4 provides access to processed RNA-seq data from all mice and human studies directly from GEO landing pages. The Cite-D-Lite extension adds buttons to export data citations to popular reference management software; whereas Datasets2Tools provides links from dataset landing pages to other pages that provide web-based interactive analysis of each dataset. In my presentation, I will demo these extensions and discuss how together these tools can enable the discovery of new knowledge.


Dr. Ma'ayan is the Director of the Mount Sinai Center for Bioinformatics and a Professor in the Department of Pharmacological Sciences. Dr. Ma'ayan is also Principal Investigator of the NIH-funded BD2K-LINCS Data Coordination and Integration Center and Mount Sinai Knowledge Management Center for Illuminating the Druggable Genome. The Ma'ayan Laboratory applies computational and mathematical methods to study the complexity of regulatory networks in mammalian cells.


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