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Bioinformatics and Computational Biology Summer Institute |
Research Projects for Fellows, June 20 - August 6, 2005
P10: Development of Rice Genome Mapper for Wheat GeneChip consensus sequences
| Title: | Development of Rice Genome Mapper for Wheat GeneChip consensus sequences |
| Mentors: | Dr. Roger Wise and Lu Hong |
| Description: | Investigators often are interested to see where all genes that are associated with a particular trait or phenotype are positioned on the genome. This is particularly beneficial for downstream analysis of GeneChip microarray data analysis. For sequenced organisms, such as rice or Arabidopsis, it is possible to see where all co-regulated genes map on the genome. However, the problem is complex for species without fully sequenced genomes, for example wheat or barley. In this case it would still be desirable to identify syntenic positions on the most closely related model genome (in this example, rice). These map locations could then be used to search for associations with trait loci to integrate gene expression data with phenotype data. We have developed a pilot Rice Genome Mapper tool for batch mapping Barley1 probe sets onto the Rice Genome Browser at Gramene [ http://cereals.vrac.iastate.edu/cgi-bin/Batch_search06.cgi]. The project is to implement Rice Genome Mapper for the 61,000 probe-set Wheat GeneChip such that data from an existing experiment in wheat development can then be positioned on the genome map. |
| Web Resources: | http://barleybase.org http://plexdb.org |
| References: | 1: Caldo, RA, D Nettleton and RP Wise. 2004. Interaction-dependent gene expression in Mla -specified response to barley powdery mildew. Plant Cell. 16: 2514-2528 2: Close, TJ, S Wanamaker, R Caldo, SM Turner, DA Ashlock, JA Dickerson, RA Wing, GJ Muehlbauer, A Kleinhofs and RP Wise. 2004. A new resource for cereal genomics: 22K barley GeneChip comes of age. Plant Physiology 134: 960-968 3: Shen, L, J Gong, RA Caldo, D Nettleton, D Cook, RP Wise, and JA Dickerson. 2005. BarleyBase-an expression profiling database for plant genomics. Nucleic Acids Research 33: D614-D618 |