Introduction: BarleyBase is a USDA-funded public repository for plant microarray data. BarleyBase is expanding to PLEXdb, the comprehensive Plant Expression Database. It now supports 11 plant microarray platforms, including the 22K Affymetrix Barley1 and Arabidopsis GeneChips. BarleyBase houses gene expression data along with experiment information. The Barley1 GeneChip was developed with the support of an international consortium of barley researchers and funding from the USDA IFAFS program.

Submission: BarleyBase is committed to making data from the Barley1 GeneChip publicly available to researchers world-wide. Researchers are encouraged to submit their data to the repository through BarleyExpress,  our MIAME-compliant online submission tool. Submitted data can be made public immediately, or an Accession no. can be acquired up to 180 days prior to publication. Submitters can also grant access to their data to designated individuals or groups, including manuscript reviewers.  Total Submissions: 2119 hybridizations from 72 experiments.

Data Access: All users can download public data, or individual files through database experiment query.  GeneChip probe sets can be searched by expression profiles, and by biological criteria including keywords, sequence, or probe set names. Interconnecting links with PlantGDB and Gramene allows users to perform gene predictions using the 21,439 Barley1 exemplar sequences, or cross-species comparison at genome level. Arabidopsis probe sets can also be accessed by pathway or gene family information.

Analysis: The first step of analysis is checking summary of experiments and their hybridizations. This will help in understanding the data to be analyzed and in quality checking. The second step is to choose an experiment, and select  interesting genes (probe sets) through filtering by expression profile or by biological criteria. Statistical test is the major tool for identifying differentially-expressed genes. The resulting gene lists are saved. At last, pattern recognition can be carried out on the saved gene lists.

Visualization: At the highest data level, box plots, histograms and scatter plots are used to check data distribution and quality across hybridizations of an experiment. Expression profile for single gene or gene list are shown as line graph or heatmap. At the lowest level, probe-level raw intensities are visualized as box plots. Probe alignment on exemplar sequences provides visualization of probe sequences. more.

Documentation: Take a Quick Tour and read tutorial on expression data access and analysis at BarleyBase. The FAQ will answer many general questions. The detailed instructions for submission, query and data analysis flow  are provided through the help pages. Download our 2005 Plant and Animal Genome Conference XIII and 2004 MGED7 posters and tutorial for submission.

Publication:  Publications relevant to BarleyBase or Barley1 GeneChip are here .

Registration: Registered users may request to join a group, thus getting access to unpublished data open only to the group members. It also allows users to keep searching and analysis results on server under their ID.

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