Advanced tools from the Shamir lab for analyzing microarrays, cis-regulation, and signaling pathways


We are pleased to announce a free, hands-on tutorial on three advanced tools for analyzing gene and microRNA expression, cis-regulatory sequences, protein networks, and other high-throughput functional genomics data.

EXPANDER is a “one-stop shop” tool for analyzing microarray data. It lets you fully analyze your gene-expression microarrays within a single tool. It comes with up-to-date data for 14 species, and more can be added as needed. It includes normalization and filtering, clustering and biclustering, and high-level analysis of functional enrichment and cis-regulatory elements. The tool’s integrated analysis capabilities and built-in support for multiple organisms make it unique among the many tools available for microarray data analysis. The latest version (V5.2) will be presented. The tutorial will show how to use EXPANDER for an end-to-end analysis of microarray data.

SPIKE is a highly curated knowledge-base of human signaling pathways. It provides pathway visualization, allows the user to interactively modify the representation of regulatory interactions, and enables superposition of functional genomic and proteomic data. Its inference engine identifies novel functional interplays between network components. The database is continually updated by community experts. SPIKE’s capabilities within the EXPANDER workflow will be demonstrated.

AMADEUS is a platform for genome-scale detection of known and novel cis-regulatory motifs, such as transcription factors and microRNA binding sites. It sets a new standard among motif-discovery software for accuracy, running time, range of applications, and ease of use.

These tools have been developed, and continue to be enhanced, in Prof. Ron Shamir’s Computational Genomics Group at Tel Aviv University; more details and downloads are available on the group’s website,

The presentation of each tool will also accompanied by a short hands-on session, in which participants will apply the tools to analyze real data.

Organizer: Prof. Ron Shamir

Instructors: Adi Maron-Katz, Eyal David, and Yaron Orenstein

Workshop date and time: Tuesday, April 12th, 2011, 10:15-15:00.

Number of Participants: up to 30 people.

Location: PC Classroom/SGI classroom, 03 Sherman Building, Tel Aviv University.

Campus map

Please note that although the workshops are free of charge, the subscription is obligatory and the registration period ends three working days before the workshop. To register, please fill the registration form.

For questions, please contact: Dr Metsada Pasmanik-Chor. Tel: 03-6406992

On the agenda:

10:15-11:00: Data, preprocessing, grouping

11:00-11:20: Hands-on part I

11:20-11:45: Group analysis

11:45-12:05: Hands-on part II

12:05 – 12:20: Coffee Break

12:20-12:50: Spike

12:50-13:10: Hands-on part III

13:10 – 14:10: Lunch Break

14:10 – 14:40: Amadeus

14:40 – 15:00: Hands-on part IV