| Abstract Detail
Bioinformatics - Afternoon Rensink, WA [1], Hart, A [1], Rehfeld, K [1], Liu, J [1], Ly, E [1], Buell, CR [1]. Conserved co-expression networks in solanaceous plant species. A large scale analysis of available Expressed Sequence Tag collections from solanaceous species revealed a high level of sequence conservation among the Solanaceae. Due to this high level of sequence conservation a single microarray platform containing ~12,000 potato clones representing ~10,000 genes can be used for different solanaceous species. Through a large number of collaborations, we have collected expression profiles for potato, tomato and several Nicotiana species addressing development, abiotic and biotic stress. The availability of a large number of expression profiles allows for the identification of transcriptional networks of co-regulated genes. A total of 661 hybridizations representing 26 independent studies were analyzed for co-expression links between the clones on the array by calculating the Pearson correlation coefficient. Over 2.5 million significant co-expression links were identified among all 26 studies. Imposing the requirement that the co-expression link was confirmed in at least eight studies, 1,755 links representing 1,010 transcripts were identified. Using the frequency of co-expression among the 26 studies, these transcripts could be clustered into several co-expressed networks. The analysis of gene ontology assignments in these networks revealed common biological functions among the transcriptional networks such as protein and amino acid metabolism, photosynthesis, as well as transcription and signal transduction. The comparison of co-expression links that were confirmed in at least two studies of tomato, potato and Nicotiana species yielded 1,183 co-expression links that were conserved among these three solanaceous species. These data indicate that the level of sequence conservation among Solanaceae also reflects functional conservation. The analysis of biotic stress experiments identified co-expression networks specific for different pathogen taxa indicating that a specific response to different pathogens is present. All expression data is available at www.tigr.org/tdb/potato.
Log in to add this item to your schedule
Related Links:
1 - The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD, 20850, US
Keywords:
co-expression
regulatory networks.
Session: SAT07-1
Location: Hall of Ideas Room E/Monona Terrace
Date: Wednesday, July 26th, 2006
Time: 1:40 PM
Abstract ID:27 |
