The workshop will familiarize researchers with advanced computational tools developed for the analysis of gene and microRNAs expression, cis-regulatory sequences, protein networks and other high-throughput functional genomic data.
These tools have been developed by the Computational Genomics group, Tel Aviv University (Ron Shamir's group). Four tools will be presented:
EXPANDER is an integrative package for the analysis of gene expression microarray data, designed as a 'one-stop shop' tool that implements various data analysis algorithms ranging from the initial steps of normalization and filtering, through clustering and biclustering, to high-level functional enrichment analysis and cis-regulatory elements analysis. The latest version of the package (V5) will be presented.
AMADEUS is a user-friendly software suite for efficient genome-scale detection of novel cis-regulatory motifs, such as transcription factors and micro-RNAs binding patterns. It supports diverse motif discovery tasks, and was shown to outperform the leading extant tools.
SPIKE is a highly curated knowledge-base of signaling pathways. It includes a database for biological signaling pathways, means for interactive visualization of these pathways, and algorithms for network analysis, aiming to discover novel functional interplays between network components.
MATISSE is a tool for integrated analysis of protein-interaction networks and gene expression patterns for the detection of 'hot spots' in the network, i.e., connected sub-networks whose components exhibit coherent expression profiles.
The workshop will consist of presentations of the tools and their capabilities. The presentation of each tool will also accompanied by a short hands-on session, in which participants will personally apply the tools to analyze real data.
Workshop Program
- 09:00 - 09:30: Expander - Part I
- 09:30 - 10:00: Expander hands-on part I
- 10:00 - 10:15: Break
- 10:15 - 10:30: Expander part II
- 10:30 - 11:00: Matisse + FAME
- 11:00 - 11:20: Spike
- 11:20 - 12:00: Expander hands-on part II (includes Matisse& Spike)
- 12:00 - 12:15: Break
- 12:15 - 12:35: Amadeus
- 12:35 - 13:00: Amadeus hands-on
For more information on all the above tools, see open in new windowhttp://acgt.cs.tau.ac.il
Organizer: Prof. Ron Shamir
Instructors (tentative list): Igor Ulitsky, Chaim Linhart, Adi Maron-Katz, Dorit Sagir, Seagull Shavit.