Transcript PLEXdb - Plant Expression Database

PLEXdb
Plant Expression database
www.plexdb.org
Ethalinda Cannon
Iowa State University
January 15th, 2007
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 longoligo designs in the future.
PLEXdb is still in development: not all tools developed
for BarleyBase.org have been ported to PLEXdb.
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
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)
Microarray annotation
Microarray annotation
Probe sequence and alignment
Exploring expression data
Expression patterns
Co-expressed genes
PLEXdb tools
• Get probe set consensus sequence
• Blast against consensus sequences
• Microarray Platform Translator (in initial
testing and review phase)
• Rice Genome Mapper
Blast against consensus sequences
Blast against consensus sequences
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).
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
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.
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.
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
1. Experiment description
2. Experiment treatment
2. Experiment treatment
2. Experiment treatment
2. Experiment treatment
2. Experiment treatment
2. Experiment treatment
3. Treatment replicates
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.
5. Sample information
Includes:
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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
6. Hybridization information
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).
Future plans
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Update and expand array annotation
Gene lists
Continue porting BarleyBase utilities
Add support for long oligo microarray
designs
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.