Web Wednesday: Interlogs

I recently learned about a new online tool and corresponding paper that the authors have used in conjunction with RNAi screen datasets obtained at the DRSC to build interaction networks.

Interlogfinder

Wiles et al. (2010) Building and analyzing protein interactome networks by cross-species comparisons. BMC Systems Biology 4;36.

RNAi Review

Excited to see this week that a PubMed search now pulls up the Mohr (that's me), Bakal & Perrimon review that we've been working on for Annual Reviews of Biochemistry.

Annu Rev Biochem. 2010 Apr 1. [Epub ahead of print]

Genomic Screening with RNAi: Results and Challenges.

Mohr S, Bakal C, Perrimon N.

Abstract: RNA interference (RNAi) is an effective tool for genome-scale, high-throughput analysis of gene function. In the past five years, a number of genome-scale RNAi high-throughput screens (HTSs) have been done in both Drosophila and mammalian cultured cells to study diverse biological processes, including signal transduction, cancer biology, and host cell responses to infection. Results from these screens have led to the identification of new components of these processes and, importantly, have also provided insights into the complexity of biological systems, forcing new and innovative approaches to understanding functional networks in cells. Here, we review the main findings that have emerged from RNAi HTS and discuss technical issues that remain to be improved, in particular the verification of RNAi results and validation of their biological relevance. Furthermore, we discuss the importance of multiplexed and integrated experimental data analysis pipelines to RNAi HTS.

Breaking Report: Genome-Wide

Just back from the fly meeting (including our successful workshop on RNAi in cells and flies--thanks to all participants!). Now it's back to work as usual, with these papers at the top of the reading pile:

A cell-based screen from the Boutros group on innate immunity:

Kuttenkeuler et al. (2010) A large-scale RNAi screen identifies Deaf1 as a regulator of innate immune responses in Drosophila. J Innate Immun. 2010 Feb;2(2):181-94. Epub 2009 Oct 13.

And an in vivo screen from the Penninger group on heart function:

Neely et al. (2010) A global in vivo Drosophila RNAi screen identifies NOT3 as a conserved regulator of heart function. Cell. 2010 Apr 2;141(1):142-53.

Live and In Person!

Myself and co-organizers L. Perkins, M. Boutros and K. Keleman are presenting a workshop in the Friday afternoon workshop session at the 51st ADRC in D.C. this week.

The lineup:

RNAi screening in cells: S. Mohr, D. Sims (FLIGHT), M. Boutros

RNAi screening in vivo: K. Keleman, F. Schnorrer, L. Perkins

Q&A to follow

The emphasis will be on available resources. We have prepared a handout of information about various resources (around the globe and online) for doing Drosophila RNAi in cells and in vivo. If we have left over copies, we will make them available at the registration desk, near the posters, or another obvious and appropriate location after the workshop.

Hope to see you there!