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PLEXdb Pl ant Ex pression d ata b ase. 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

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Plexdb pl ant ex pression d ata b ase

PLEXdb Plant Expression database

www.plexdb.org

Ethalinda Cannon

Iowa State University

January 15th, 2007


A brief history of plexdb
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.


Plexdb objectives
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
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)








Plexdb tools
PLEXdb tools

  • Get probe set consensus sequence

  • Blast against consensus sequences

  • Microarray Platform Translator (in initial testing and review phase)

  • Rice Genome Mapper




Why submit experiments to plexdb
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
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
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
PLEX Express

  • Experiment background information.

  • Describe experiment treatment as one or more factors and levels (e.g. ?).

  • Give replicate counts for each treatment

  • Upload hybridization data files (for Affymetrix GeneChips CEL and EXP files are required).

  • Describe all plant samples.

  • Assign data files and samples to each hybridization.


1 experiment description
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










4 upload data files
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
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



After finalizing your experiment
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
Future plans

  • Update and expand array annotation

  • Gene lists

  • Continue porting BarleyBase utilities

  • Add support for long oligo microarray designs


Credits and acknowledgements
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.


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