| 1. |
- Lindlöf, Angelica, et al.
(författare)
-
Identification of Cold-Induced Genes in Cereal Crops and Arabidopsis Through Comparative Analysis of Multiple EST Sets
- 2007
-
Ingår i: S. Hochreiter and R. Wagner (Eds.): BIRD, LNBI. - Berlin, Heidelberg : Springer. ; 4414, s. 48-65, s. 48-65
-
Tidskriftsartikel (refereegranskat)abstract
- Freezing tolerance in plants is obtained during a period of low nonfreezing temperatures before the winter sets on, through a biological process known as cold acclimation. Cold is one of the major stress factors that limits the growth, productivity and distribution of plants, and understanding the mechanism of cold tolerance is therefore important for crop improvement. Expressed sequence tags (EST) analysis is a powerful, economical and timeefficient way of assembling information on the transcriptome. To date, several EST sets have been generated from cold-induced cDNA libraries from several different plant species. In this study we utilize the variation in the frequency of ESTs sampled from different cold-stressed plant libraries, in order to identify genes preferentially expressed in cold in comparison to a number of control sets. The species included in the comparative study are oat (Avena sativa), barley (Hordeum vulgare), wheat (Triticum aestivum), rice (Oryza sativa) and Arabidopsis thaliana. However, in order to get comparable gene expression estimates across multiple species and data sets, we choose to compare the expression of tentative ortholog groups (TOGs) instead of single genes, as in the normal procedure. We consider TOGs as preferentially expressed if they are detected as differentially expressed by a test statistic and up-regulated in comparison to all control sets, and/or uniquely expressed during cold stress, i.e., not present in any of the control sets. The result of this analysis revealed a diverse representation of genes in the different species. In addition, the derived TOGs mainly represent genes that are long-term highly or moderately expressed in response to cold and/or other stresses.
|
|
| 2. |
- Lubovac, Zelmina, et al.
(författare)
-
Weighted Cohesiveness for Identification of Functional Modules and their Interconnectivity
- 2007
-
Ingår i: Bioinformatics Research and Development. - Berlin, Heidelberg : Springer. - 9783540712329 - 9783540712336 ; , s. 185-198
-
Konferensbidrag (refereegranskat)abstract
- Systems biology offers a holistic perspective where individual proteins are viewed as elements in a network of protein-protein interactions (PPI), in which the proteins have contextual functions within functional modules. In order to facilitate the identification and analysis of such modules, we have previously proposed a Gene Ontology-weighted clustering coefficient for identification of modules in PPI networks and a method, named SWEMODE (Semantic WEights for MODule Elucidation), where this measure is used to identify network modules. Here, we introduce novel aspects of the method that are tested and evaluated. One of the aspects that we consider is to use the k-core graph instead of the original protein-protein interaction graph.Also, by taking the spatial aspect into account, by using the GO cellular component annotation when calculating weighted cohesiveness, we are able to improve the results compared to previous work where only two of the GO aspects (molecular function and biological process) were combined. We here evaluate the predicted modules by calculating their overlap with MIPS functional complexes. In addition, we identify the “most frequent” proteins, i.e. the proteins that most frequently participate in overlapping modules. We also investigate the role of these proteins in the interconnectivity between modules. We find that the majority of identified proteins are involved in the assembly and arrangement of cell structures, such as the cell wall and cell envelope.
|
|
