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NetEffects: Analysing the effects of gene perturbations on longevity via the Insulin Pathway

Introduction

Pathways represent sequences of reactions that take place in a coordinated manner. Our methods, implemented in NetEffects, analyse the effects of perturbations of specific pathway components to the rest of the pathway and especially the biological processes that it controls. The examples below focuses on the Insulin/Insulin-like Growth Factor Signalling Pathway in Drosophila melanogaster and Caenorhabtitis elegans and their role in lifespan. NetEffects provides two different ways of studying each pathway:

  1. Querying it by up- or down-regulating specific components.
  2. Importing gene expression data and phenotype information (lifespan extension/reduction) and inferring the effects on the pathway.

The underlying methodology used is Answer Set Programming (ASP), a form of declarative programming. We use the ASP tools gringo and clasp that are available by Potassco, the Potsdam Answer Set Solving Collection.

Currently available pathways for analysis

The Insulin/Insulin-like Growth Factor Signaling Pathway in Caenorhabtitis elegans.

The Insulin/Insulin-like Growth Factor Signaling Pathway in Drosophila melanogaster.

The Insulin/Insulin-like Growth Factor Signaling Pathway in Mus musculus.

How to cite NetEffects

Using Answer Set Programming to Integrate RNA Expression with Signalling Pathway Information to Infer How Mutations Affect Ageing, I Papatheodorou, M Ziehm, D Wieser, N Alic, L Partridge, JM Thornton. PloS one 7 (12), e50881

Feedback, suggestions, questions

Please contact Irene Papatheodorou by email.

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