Gene Expression Networks Esra Erdin CS 790g Fall 2010

Introduction Project Description Methodology 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 they are affected adversely by these factors.

Adapted from

Human life will also be affected negatively as a result of adverse effects that plants encounters.

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.

Methodology What will I do during my project?  Data collection 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? Microarray technique for gene expression profiles DNA Microarrays KhM

How will I collect them? Collect data from biological databases

NCBI: National Center for Biotechnology Information 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.

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 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 re- annotated Archive data which can be queried for individual gene expression under different biological conditions across experiments

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 Gramene

Published papers

Kawasaki et al. Gene Expression Profiles during the Initial Phase of Salt Stress in Rice.

Qin et al. Heat stress-responsive transcriptome analysis in heat susceptible and tolerant wheat

Wang et al. Temporal progression of gene expression responses to salt shock in maize

Some diffuculties being encountered during data collection period:  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.

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

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

Black edges represent the relation of genes under stress factor 1 Blue edges represent the relation of genes under stress factor 2 The yellow dotted genes are the ones tolerant to both stress factors.

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.

References 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.