Integrative transcriptomic approaches to analyzing plant co-expression networks

It is well documented that transcriptionally coordinated genes tend to be functionally related, and that such relationships may be conserved across different species, and even kingdoms. (Ihmels et al., 2004). Such relationships was initially utilized to reveal functional gene modules in yeast and mammals (Ihmels et al., 2004), and to explore orthologous gene functions between different species and kingdoms (Stuart et al., 2003; Bergmann et al., 2004). Model organisms, such as Arabidopsis, are readily used in basic research due to resource availability and relative speed of data acquisition. A major goal is to transfer the acquired knowledge from these model organisms to species that are of greater importance to our society. However, due to large gene families in plants, the identification of functional equivalents of well characterized Arabidopsis genes in other plants is a non-trivial task, which often returns erroneous or inconclusive results. In this thesis, concepts of utilizing co-expression networks to help infer (i) gene function, (ii) organization of biological processes and (iii) knowledge transfer between species are introduced. An often overlooked fact by bioinformaticians is that a bioinformatic method is as useful as its accessibility. Therefore, majority of the work presented in this thesis was directed on developing freely available, user-friendly web-tools accessible for any biologist.

Level thesis:degree_level

thesis.doctoral

Grantor dc:publisher

Universität Potsdam

Year

2011

Author dc:creator

• Mutwil, Marek

Contributors dc:contributor

• Bock, Ralph

• Koexpression
• vergleichend
• Transkriptom
• co-expression
• comparative
• transcriptomics

Statement dc:rights

• Creative Commons - Namensnennung - Nicht-kommerziell - Weitergabe unter gleichen Bedingungen 3.0 Unported

Repository record source_url

https://publishup.uni-potsdam.de/frontdoor/index/index/docId/4862

OAI identifier oai:identifier

oai:kobv.de-opus4-uni-potsdam:4862