Ghent University Academic Bibliography

Advanced

Comparative transcriptomics in plants

Movahedi, Sara (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
publication status
published
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
2017-01-16 10:40:35
@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.