Section outline

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    Inferring gene regulatory networks from high-throughput data with ISMARA

    23 May 2018

    University of Basel, Biozentrum, room Sky Lounge

    This page is addressed to registered participants. To access course description and application form, please click here.

    For any assistance, please contact training@sib.swiss.

  • Schedule

    9:00 – 10:30 Introduction to Motif Activity Response Analysis. Transcription factor binding site predictions, processing of raw RNA-seq and ChIP-seq data, and the MARA model. Users that brought their own data can upload them to the webserver.


    10:30 – 11:00 Coffee break


    11:00 – 12:30 Using ISMARA: data types that are supported, and usage of the ISMARA client or direct upload. Overview of the basic results that ISMARA provides: Lists of key regulators, their activities, lists of target genes, and core networks.


    12:30 – 13:30 Lunch break


    13:30 – 15:00 Advanced interactive features of ISMARA. Exploring the regulation of particular target genes. Pathways targeting by particular regulators. Averaging across replicate samples. Calculating contrasts between subsets of samples.


    15:00 – 15:30 Coffee break


    15:30 – 17:00 Users explore results on their own datasets (or provided test datasets for users that did not bring their own data). Tutors provide guidance.

  • Materials