Transcript Gene Expression Networks

Gene Expression Networks
Esra Erdin
CS 790g
Fall 2010





Introduction
Project Description
Related Work
Conclusion
References
Introduction

Plants have important role in the lives of
organisms

Plant growth in the natural environment is
affected by a number of factors.

We call these factors stresses.

These include environmental factors such as
low temperature, heat, drought, wind,
ultraviolet light, anoxia and high salinity and
biological factors such as pathogens
(bacteria, viruses, fungi)

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=1518

Human life will also be affected negatively as
a result of adverse effects that plants
encounters.

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.

When this behavior is analyzed and obtained
it is important and now easy to develop and
improve stress tolerance in crops. This has
significant implications for people and
farmers worldwide.
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.
Related Work
“Similarities and differences of gene
expression in yeast stress conditions”,
Rokhlenko O, Wexler Y, Yakhini Z

They studied stress response mechanisms
in Saccharomyces cerevisiae by identifying
genes that, according to very stringent
criteria, have persistent co-expression
under a variety of stress conditions.


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-coexpression graphs of 19 stress conditions. The tree was constructed using an
average-linkage neighbor-joining method.

As a result of their method they detected
cliques in the intersection graphs that are
much larger than expected under a null
model of changing gene identities for different
stress conditions but keeping the coexpression topology within each one. They
also showed the genes of many cliques in the
intersection graphs are co-localized in the
yeast genome.
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.

They found many stress-responsive genes as
a result of their study. They also discover
several transcription factor genes as well as
pseudegenes and transposons that have
been missed in previous analyses with
standard expression arrays.
Conclusion

Developing stress tolerant crops by modifying
the genes that are co-expressed under all
stress conditions is a crucial topic.

To be able to develop stress tolerant genes,
their analysis should be done properly.


Gasch,A. et al. (2000) Genomic expression
programs in the response of yeast cells to
environmental changes. Mol. Biol. Cell, 11,
4241–4257.
Zeller G, Henz SR, Widmer CK,
Sachsenberg T, Ratsch G, Weigel D,
Laubinger S.(2009) Stress-induced
changes in the Arabidopsis thaliana
transcriptome analyzed using wholegenome tiling arrays.