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Comparative transcriptomics in plants

Sara Movahedi UGent (2012)
abstract
Comparative genomics is the study of the structural and functional rela- tionships between the genomes of different species or strains. Recently microarray experiments have yielded massive amounts of expression infor- mation for many genes under various conditions or in different tissues for different model species. Expression compendia grouping multiple microar- ray experiments performed in similar (or different) experimental condition make it possible to define correlated expression patterns between genes. Genes within such a coexpression cluster are expected to have more similar functionality compared to genes lacking expression similarity. In this thesis the different steps required to systematically compare expres- sion data across species are described and some future applications of plant comparative transcriptomics are highlighted. Then we analyzed if function- ally related genes show coexpression in Arabidopsis and rice and developed a general framework to measure expression context conservation (ECC) for orthologous genes. Additionally, we studied the evolutionary parameters influencing ECC conservation and compared expression with sequence evo- lution. At the end, a new method is presented to define high quality tis- sue specific genes in seven different plant species; A.thaliana (Arabidopsis), Z.mays (Maize), M.truncatula (Medicago), P.trichocarpa (Poplar), O.sativa (Rice), G.max (Soybean) and V.vinifera (Grape) using Affymetrix microar- ray expression profiles. We also performed an in-depth study on the rela- tionship between leaf tissue specific genes coexpression clusters, within a species and in comparison with other species for a set of strictly selected genes.
Please use this url to cite or link to this publication:
author
promoter
UGent and UGent
organization
year
type
dissertation (monograph)
subject
pages
XIV, 144 pages
publisher
Ghent University. Faculty of Sciences
place of publication
Ghent, Belgium
defense location
Zwijnaarde : Technologiepark (FSVM building)
defense date
2012-06-08 16:00
language
English
UGent publication?
yes
classification
D1
additional info
dissertation consists of copyrighted material
copyright statement
I have transferred the copyright for this publication to the publisher
id
3005592
handle
http://hdl.handle.net/1854/LU-3005592
date created
2012-10-03 16:23:09
date last changed
2012-10-05 09:41:41
@phdthesis{3005592,
  abstract     = {Comparative genomics is the study of the structural and functional rela- tionships between the genomes of different species or strains. Recently microarray experiments have yielded massive amounts of expression infor- mation for many genes under various conditions or in different tissues for different model species. Expression compendia grouping multiple microar- ray experiments performed in similar (or different) experimental condition make it possible to define correlated expression patterns between genes. Genes within such a coexpression cluster are expected to have more similar functionality compared to genes lacking expression similarity. 
In this thesis the different steps required to systematically compare expres- sion data across species are described and some future applications of plant comparative transcriptomics are highlighted. Then we analyzed if function- ally related genes show coexpression in Arabidopsis and rice and developed a general framework to measure expression context conservation (ECC) for orthologous genes. Additionally, we studied the evolutionary parameters influencing ECC conservation and compared expression with sequence evo- lution. At the end, a new method is presented to define high quality tis- sue specific genes in seven different plant species; A.thaliana (Arabidopsis), Z.mays (Maize), M.truncatula (Medicago), P.trichocarpa (Poplar), O.sativa (Rice), G.max (Soybean) and V.vinifera (Grape) using Affymetrix microar- ray expression profiles. We also performed an in-depth study on the rela- tionship between leaf tissue specific genes coexpression clusters, within a species and in comparison with other species for a set of strictly selected genes.},
  author       = {Movahedi, Sara},
  language     = {eng},
  pages        = {XIV, 144},
  publisher    = {Ghent University. Faculty of Sciences},
  school       = {Ghent University},
  title        = {Comparative transcriptomics in plants},
  year         = {2012},
}

Chicago
Movahedi, Sara. 2012. “Comparative Transcriptomics in Plants”. Ghent, Belgium: Ghent University. Faculty of Sciences.
APA
Movahedi, S. (2012). Comparative transcriptomics in plants. Ghent University. Faculty of Sciences, Ghent, Belgium.
Vancouver
1.
Movahedi S. Comparative transcriptomics in plants. [Ghent, Belgium]: Ghent University. Faculty of Sciences; 2012.
MLA
Movahedi, Sara. “Comparative Transcriptomics in Plants.” 2012 : n. pag. Print.