ISMARA - The Integrated System for Motif Actitivity Response Analysis is a free online tool that models genome-wide expression data, or any other quantitative signal along the genome, in terms of the local occurrence of computationally predicted regulatory sites for transcription factors (TFs) and micro-RNAS (miRNAs).
The only input required for running ISMARA is either expression data (microarray CEL files or RNA-seq BED files), or ChIP-seq data (BED files), from a set of biological samples.
As a result, ISMARA will infer which regulators are most important for explaining the input data, i.e. either variation in expression levels or ChIP-seq signal along the genome, as well as detailed predictions of the regulatory role of each regulator. Results include, for each regulatory motif, inferred activities across the input samples, predicted genome-wide targets, enriched pathways and functional classes of genes, and direct interactions between regulators. All results are presented within interactive and easily navigable HTML pages. The full results are also available for download.
More extensive documentation and sample input data are provided under the "Usage" link.
The only input required to run ISMARA is either a set of microarray CEL files (gene expression data) or a set of BED files (either RNA-seq or ChIP-seq data). Example input files are presented below. ISMARA normalizes all input data, and then uses them to calculate a quantitative `signal' associated with each promoter in the genome. ISMARA then models the promoter signals across the samples in terms of computationally predicted transcription factor binding sites in the neighborhood of the promoter (and also miRNA binding sites in the 3' UTRs of transcripts when analyzing gene expression data). As a result, ISMARA predicts the genome-wide regulatory interactions that explain the provided input data. These results include quantification of the importance of each regulator in explaining the input data, the activity of each regulator across the input samples, genome-wide targets of each regulator, direct interactions between regulators, and so on. A more extensive description of the results is provided here.
Please submit the input files (CEL, BED) to the form above. Files can be submitted one by one or compressed into an archive (zip, tar.gz). To receive automatic notification when ISMARA has finished analyzing the data, please enter your email address in the provided form. After this, press the "Start upload" button. You will then be redirected to a page which shows the current status of your job. If you have not provided an email address, please make sure to bookmark or save the URL of this page!
ISMARA accepts two file formats. CEL files for microarray data and BED files for RNA-Seq and Chip-Seq data (see the sample data below). If you have more than 5 files, it is most practical to put all CEL/BED files into archive (zip, tar.gz, tar.bz2) and submit this archive to ISMARA. Note, the archive should contain just CEL/BED files no folders or subfolders.
An "Expert" mode is available for experienced users that want to run ISMARA with individually defined sets of genomic regions and/or their own regulatory site predictions. An explanation is available here.
Currently nine human and eleven mouse Affymetrix Gene Chips™ are supported.
A description of the results that ISMARA provides is given here.