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.