Plexdb pl ant ex pression d ata b ase
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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)


Microarray annotation

Microarray annotation


Microarray annotation1

Microarray annotation


Probe sequence and alignment

Probe sequence and alignment


Exploring expression data

Exploring expression data


Expression patterns

Expression patterns


Co expressed genes

Co-expressed genes


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


Blast against consensus sequences

Blast against consensus sequences


Blast against consensus sequences1

Blast against consensus sequences


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


1 experiment description1

1. Experiment description


2 experiment treatment

2. Experiment treatment


2 experiment treatment1

2. Experiment treatment


2 experiment treatment2

2. Experiment treatment


2 experiment treatment3

2. Experiment treatment


2 experiment treatment4

2. Experiment treatment


2 experiment treatment5

2. Experiment treatment


3 treatment replicates

3. Treatment replicates


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


6 hybridization information

6. Hybridization 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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