Analyzing Gene Expression Networks in Rice, Wheat, and Maize for Crop Stress Tolerance, Slides of Computer Networks

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Gene Expression Networks

• Introduction
• Project Description
• Related Work
• Conclusion
• References

• Plant growth in the natural environment is affected by a number of factors.
• We call these factors stresses.

• Every organism gives different responses to different stresses they are subjected to.
• However generally the plants they are affected adversely by these factors.

• Adapted from http://agdev.anr.udel.edu/weeklycropupdate/?p=

• Crop losses due to these stresses are in the billions of dollars annually. It has been estimated that stress factors depress the yield of agronomically important crops in the United States by 78%, of which about 70% is due to unfavorable environmental conditions.

• Because crops have importance in human life, it is a crucial issue to understand the behavior of crops under any stress factors.

Project Description

• The analysis of stress tolerance of crops; rice, wheat and maize under drought, high salinity and low temperature.

• Collect data from studies that are published
• Analyse sets of genes that give any response to these stresses separately.
• For every stress condition there will be an undirected graph whose vertices correspond to genes, and the vertices of two genes are connected by an edge if their expressions are correlated.
• Apply the network metrics on these graphs I constructed.

• To study the relationship of different stress conditions they constructed co-co-expression graphs for each pair of conditions.
• They make a fast clique search method to the intersection of several co-expression graphs calculated over data.

A hierarchical tree representing the distances in terms of number of edges in co-co- expression graphs of 19 stress conditions. The tree was constructed using an average-linkage neighbor-joining method.

Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays, Zeller G, Henz SR, Widmer CK, Sachsenberg T, Ratsch G, Weigel D, Laubinger S.(2009)

• They used whole-genome tiling arrays to analyze the effects of salt, osmotic, cold and heat stres to provide an exthaustive view of stres-induced changes.