1. PLEXdb Plant Expression database Ethalinda Cannon Iowa State University www.plexdb.org January 15th, 2007

2. A brief history of PLEXdb (2003 - 2005) BarleyBase.org Focus was on the Barley1 and ATH1 Affymetrix GeneChips (2005 - ) PLEXdb.org Expanded to include all plant and plant pathogen Affymetrix GeneChips with plans to support long- oligo designs in the future. PLEXdb is still in development: not all tools developed for BarleyBase.org have been ported to PLEXdb.

3. PLEXdb objectives provide annotation for all plant and plant pathogen microarrays available from Affymetrix serve as a repository for plant microarray experiments, especially grains, legumes and grape provide means to explore expression and sequence data

4. PLEXdb provides: annotation for 15 microarrays, representing 12 organisms analysis and visualization tools experiment data submission, normalization, browsing, downloading - 43 public experiments and 2200 hybridizations now available in database gene lists (not yet available)

9. Microarray annotation

11. Probe sequence and alignment

12. Exploring expression data

13. Expression patterns

14. Co-expressed genes

15. PLEXdb tools Get probe set consensus sequence Blast against consensus sequences Microarray Platform Translator (in initial testing and review phase) Rice Genome Mapper

17. Blast against consensus sequences

19. Why submit experiments to PLEXdb? Journals and funding agencies require that data be made available. Verify the completeness of your experiment information. Serves as a safe repository for your data. Provides means of exploring your data. Increase the impact of your research (BB1 data has been downloaded 133 times).

20. Barley Express to PLEX Express The danger of being an early adopter: things change You never get things right the first time Difficult to predict the future; size of large experiments greater than anticipated The user is always right PLEX Express is in its initial testing and review phase

21. The New PLEX Express Revised database design to better meet MIAME, MIAME/Plant, and SOFTtext requirements and to accommodate larger experiments. Closer ties to current Plant Ontology terms. Easier to use, although it requires in-depth information so submitting an experiment is still time-consuming. Will submit experiments to GEO at the request of the submitter. Improved, streamlined normalization process. Relies on standard ftp for uploading data.

22. PLEX Express 1.Experiment background information. 2.Describe experiment treatment as one or more factors and levels (e.g. ?). 3.Give replicate counts for each treatment 4.Upload hybridization data files (for Affymetrix GeneChips CEL and EXP files are required). 5.Describe all plant samples. 6.Assign data files and samples to each hybridization.

23. 1. Experiment description Visibility (private, public, group consortium) Experiment name Experiment type(s) Experiment description Array design Type of replicates (biological replicates, technical replicates) Publication Experimenter

24. 1. Experiment description

25. 2. Experiment treatment

31. 3. Treatment replicates

32. 4. Upload data files You will have received ftp instructions via e-mail by this point. Data files may be uploaded individually or in one or more standard compressed formats such as gzipped or zipped files.

33. 5. Sample information Includes: –Short sample name –Sample image –Dates –Sample description –Germplasm information –Cell type or target cell type –Development stage –Growth information –Environmental conditions –Protocols –Provider information

34. 6. Hybridization information

35. After finalizing your experiment You can no longer edit your experiment yourself. You will be assigned an accession number. If you have granted the curator access, your experiment data will be hand-checked for possible errors. Your data will be normalized. Your experiment data will be made available according to your request (private, visible to your research group, public).

36. Future plans Update and expand array annotation Gene lists Continue porting BarleyBase utilities Add support for long oligo microarray designs

37. Credits and Acknowledgements Principal investigator - Julie Dickerson Co-investigators - Roger Wise, Volker Brendel BarleyBase.org - Lishuang Shen Advice, consultation & blast data - Nick Lauter, Matt Moscou Programmers - Jianqiang Xin, Ajani Thomas, Yogesh Nadkarni, Xiaokang Pan Data curator - Sudhansu Dash Partner websites and databases: PlantGDB, Gramene, GrainGenes The PLEXdb project is funded by PLEXdb is hosted at the Iowa State University Virtual Reality Applications Center.