Gene Expression Networks
Esra Erdin
CS 790g
Fall 2010
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Introduction
Project Description
Methodology
Conclusion
References
Introduction
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Plants have important role in the lives of
organisms
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Plant growth in the natural environment is
affected by a number of factors.
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We call these factors stresses.
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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)
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Every organism gives different responses to
different stresses they are subjected to.
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However generally they are affected
adversely by these factors.
Adapted from http://agdev.anr.udel.edu/weeklycropupdate/?p=1518
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Human life will also be affected negatively as
a result of adverse effects that plants
encounters.
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Because crops have importance in human
life, it is a crucial issue to understand the
behavior of crops under any stress factors.
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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
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The analysis of stress tolerance of crops;
rice, wheat and maize under drought, high
salinity and low temperature.
Methodology
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What will I do during my project?
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Data collection
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Plant gene databases
Published papers that provide data
Implement data as a network and analyse sets of
genes that give any response to these stresses
separately
Apply network metrics
How do researchers provide data?
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Microarray technique for gene expression
profiles
DNA Microarrays
http://www.youtube.com/watch?v=VNsThMNj
KhM
How will I collect them?
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Collect data from biological databases
NCBI: National Center for Biotechnology
Information
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The National Center for
Biotechnology Information
(NCBI) is part of the United
States National Library of
Medicine (NLM), a branch of
the National Institutes of
Health.
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The NCBI houses genome sequencing data
in GenBank and an index of biomedical
research articles in PubMed Central and
PubMed, as well as other information
relevant to biotechnology. All these
databases are available online through the
Entrez search engine.
Array Express Archieve
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The ArrayExpress Archive is a database of
functional genomics experiments including
gene expression where you can query and
download data collected to MIAME and
MINSEQE standards. Gene Expression
Atlas contains a subset of curated and reannotated Archive data which can be queried
for individual gene expression under different
biological conditions across experiments
Gramene
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Gramene's purpose is to provide added
value to data sets available within the public
sector, which will facilitate researchers' ability
to understand the grass genomes and take
advantage of genomic sequence known in
one species for identifying and understanding
corresponding genes, pathways and
phenotypes in other grass species.
rice, maize, sorghum, barley, oats, wheat,
and rye
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Published papers
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Kawasaki et al.
Gene Expression Profiles during the Initial
Phase of Salt Stress in Rice.
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Qin et al.
Heat stress-responsive transcriptome
analysis in heat susceptible and tolerant
wheat
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Wang et al.
Temporal progression of gene expression
responses to salt shock in maize
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Some diffuculties being encountered during
data collection period:
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Same genes must be analysed to make a feasible
comparison between plants
Genes should be subjected to same amount of
stress factors during their experiment.
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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.
Gene
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To be able to compare the genes in different
plants it is important to analyse the behaviors
of same genes in each plant.
Once we constructed the graph for first stress
then apply the second stress factor on these
and find maximum k-clique in new graph.
Coexpression graphs of genes under stress factors 1 and 2
The yellow dotted genes are
the ones tolerant to both
stress factors.
Black edges represent the relation of genes under stress factor 1
Blue edges represent the relation of genes under stress factor 2
Conclusion
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Developing stress tolerant crops by modifying
the genes that are co-expressed under all
stress conditions is a crucial topic.
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To be able to develop stress tolerant genes,
their analysis should be done properly.
References
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Wang H, Miyazaki S, Kawai K, Deyholos M,
galbraith DW, Bohnert HJ. Temporal progression
of gene expression responses to salt shock in
maize
Kawasaki S, Borchert C, Deyholos M, Wang H,
Brazille S, Kawai K, Galbraith D, Bohnert HJ.
Gene Expression Profiles during the Initial Phase
of Salt Stress in Rice.
Ergen NZ, Thimmapuram J, Bohnert HJ, Budak
H. Transcriptome pathways unique to dehydration
tolerant relatives of modern wheat.