ISMARA
MARA (motif activity response analysis) is the name given to the method developed by Piotr Balwierz and Erik van Nimwegen for explaining changes in transcript expression through the activity of transcription factors and miRNAs.
ISMARA (Integrated System for MARA) is a fully integrated server which automatically processes input data, computes TF motif activities and produces a large range of complementary data to help interpret and navigate the results. This includes:
- information about activity/mRNA expression correlation
- target promoters/genes
- first-level regulatory networks
- over-represented GO categories
- known interactions between target genes
Input data types:
- microarray (Affymetrix chips for human and mouse)
- RNA-seq
- ChIP-seq (in this case ISMARA models ChIP-seq signal changes across conditions in terms of TFBSs)
- hCAGE (currently done manually upon reques given a list of sample IDs)
ISMARA and the FANTOM5 timecourses
ISMARA has been run on all the human and mouse timecourses in FANTOM5. The results pages are linked from each timecourse's page on this wiki.
Further information
The webserver where you can upload files and view results is located at http://ismara.unibas.ch There are links to already processed example data sets (public data) and a FAQ.
A basic introduction to ISMARA can be found in this presentation:
File:301012 MARA F5TC.pdf
ISMARA manuscript is in preparation.
The result from this analysis are being used for TF network prediction, which you can read about here.
For further information, please contact
- Peter Pemberton-Ross, peter.pemberton-ross@unibas.ch
- Piotr Balwierz, piotr.balwierz@unibas.ch
