News

03/21/06

• New Fusarium data sets were released from Dr.Gary Muehlbauer, whose PLEXdb accession numbers including: FG1, FG2, FG3, FG4. Please see the publication: Guldener U, Seong KY, Boddu J, Cho S, Trail F, Xu JR, Adam G, Mewes HW, Muehlbauer GJ, Kistler HC.,Development of a Fusarium graminearum Affymetrix GeneChip for profiling fungal gene expression in vitro and in planta.Fungal Genetics and Biology. 2006 Mar 10.

03/08/06

• PLEXdb BLAST was updated. You can now search your sequences against all species in PLEXdb.

03/01/06

• New Barley1 data set, Accession number: BB8, released from Gary Muehlbauer. Please see PubMed at Expression of barley genes in wheat-barley chromosome addition lines.

2/17/06

• New Probe set annotation links to PlantGDB-assembled Unique Transcripts (PUT) assemblies.

  The probe locations for the Affymetrix GeneChip and long-oligo array designs in PLEXdb are linked to the PlantGDB PUT assemblies and to the original assemblies. These links allow investigators to examine the historical data used to design the GeneChips as well as the most up-to-date EST assemblies that support the probe sets.

2/06/06

• Exemplar annotation and Probe alignment for Affymetrix Poplar Genome Array (Populus sp 61K) are available.

01/16/06

• Annotations for species were updated.
• The tools: Data Access->Experiments-> Hybridizations/Visualization were updated. Scatter plot tool is available.
• The tool: Data Access->Genelists-> Analysis is available.
• Rice Genome Mapper was updated again with stronger features: Barley genechip alignment (Barley1_22K), Maize_18K, Maize_58K, Rice_57K and Wheat_61K data are available to query. Tutorial was updated from pdf to html format.

12/29/05                                                                                                             

• Functionalize Expression (FuncExpression) now supports all the  EUKARYOTIC and PROKARYOTIC gene expression analysis arrays listed at Affymetrix Support Page, for which Affymetrix provides Gene Ontology annotations. 

12/20/04                                                                                                             

• "BarleyBase—an expression profiling database for plant genomics", the first  paper on BarleyBase is published by Nucleic Acids Research, 2005, Vol. 33, Database issue D614-D618.
  
• Please cite BarleyBase using this paper if your publication use tools and data from BarleyBase.

12/20/04                                                                                                             

• Exemplar annotation for 22k ATH1-121501 Arabidopsis GeneChip are added
• Exemplar annotation and Probe alignment for 8k CornChip0 pilot Corn GeneChip are added.

12/14/04                                                                                                             

• Exemplar annotation and Probe alignment for 61k Wheat GeneChip are added.
• We now support the 61k Wheat GeneChip. The Wheat Genome Array  contains 61,127 probe sets representing 55,052 transcripts for all 42 chromosomes in the wheat.

12/01/04                                                                                                             

• Exemplar annotation and Probe alignment for 61k Soybean GeneChip are added.

11/29/04                                                                                                             

• Exemplar annotation and Probe alignment for 16k Grape Vitis_vinifera GeneChip are added.

11/14/04                                                                                                             

• Functionalize Expression (FuncExpression) is added for two way-integration of gene functional annotation and the gene expression data. Multiple gene lists can be classified, compared and visualized. The gene function information includes the gene ontology classification, InterPro protein functional domain prediction, metabolic pathway and gene family information. FuncExpression will support all microarray platforms in BarleyBase.

11/04/04                                                                                                             

• BarleyBase reached a new milestone today. BarleyBase now houses 28 experiment submissions, totaling 1,067 hybridizations. The hybridizations include 450 Barley1 GeneChips, 569 Arabidopsis ATH1 or AG GeneChips, and 48 Maize pilot GeneChips.

  BarleyBase is now among the largest plant microarray data repositories. Powered with our set of data mining tools, we are working towards cross-species meta analysis for plant microarray data.

  We thank all the investigators who submitted their valuable original data. We also thank to NASCArray, TAIR, TIGR and GEO for sharing their  microarray data. Special thanks to Drs. Roger Wise and Rico Caldo, who have submitted 300 Barley1 GeneChip data.

11/04/04                                                                                                             

• Enhancement on Pattern Recognition: Now users can limit analysis to only selected factor levels. This is useful for refined analysis in complex, multi-factor experiments.
• Enhancement on Gene List Creation: Now support query for MAS5 Present/Absent/Marginal Calls.

10/25/04                                                                                                             

• Drs. Diane Bassham and Tony Contento provide a new experiment, AT8: Expression analysis of Arabidopsis suspension cells during sucrose starvation, for public access. This is an ATH1 GeneChip based experiment.

10/23/04                                                                                                             

• Two new plant Affymetrix GeneChips will be supported by BarleyBase. They are both designed by Affymetrix as part of the Affymetrix® GeneChip Consortia Program.
• The GeneChip® Soybean Genome Array includes over 37,500 soybean (Glycine max) transcripts. The array also contains transcripts for two soybean pathogens:  approximately 15,800 transcripts for Phytophthora sojae a and 7,500 transcripts for Heterodera glycines (cyst nematode pathogen). It is an 11-probe pair, 11-micron format chip.
• The GeneChip® Vitis vinifera Genome Array  included 14,000 V. vinifera transcripts and 1,700 transcripts from other Vitis species, with 16 pairs of oligonucleotide probes for each sequence represented.

09/20/04                                                                                                             

• Another paper based on experiment BB4, authored by Drs. Rico Caldo, Dan Nettleton and Roger Wise, was published in The Plant Cell 16:2514-2528 (2004):  Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildew. It was commented by Editor Nancy A. Eckardt: Cutting Edge Transcriptome Analysis: It's All about Design.

08/25/04

• Two new functions added:
  1. "Gene Ontology Browser" added under "Database Overview". Gene ontology will be integrated with microarray data analysis in future, to provide high level function view on the gene list.
  2. "Download Sequences for a Gene List" added under "Probe Set Info".

08/18/04

• Experiment BB4 was kindly made open to public by Drs. Roger Wise and Rico A. Caldo. This 108-chip experiment is invaluable for barley community in evaluating Barley1 GeneChip and in pathogen resistance research.

07/29/04

• We have the second Barley1 GeneChip experiments publicly accessible online. BB5, A Ca2+/calmodulin-dependent protein kinase required for symbiotic nodule development: Gene identification by transcript-based cloning. It was kindly submitted by Mr. James Hadfield from John Innes Center, UK.

07/14/04

• Maize pilot GeneChip, CornChip0,  finished lab evaluation at Dr. Roger Wise's lab. The data will be available to public soon. This is an Affymetrix effort of designing GeneChip for highly-polymorphic species.

06/10/04

• A comprehensive Arabidopsis plant development gene expression atlas experiment is input into BarleyBase from TAIR. The experiment consisted of 280 hybridizations from different development stages. The data is stored under AT4 and AT5.

04/29/04

• We successfully migrate to new server. The BarleyBase URLs are now www.barleybase.org. The new server is almost twice as fast as previous server.

03/22/04

• "A New Resource for Cereal Genomics: 22K Barley GeneChip Comes of Age.",  the first paper detailing development of Barley1 GeneChip, was published at Plant Physiology.

03/12/04

• BarleyExpress  improved by (1). Adding support to Arabidopsis plant ontologies to sample preparation pages and (2). Revision on submission flow's sample preparation part.
• First batch of  six Arabidopsis experiments from NASCArrays are deposited into BarleyBase for public access.  More being added.

02/18/04

• Statistical test methods for finding differentially expressed genes added. More complex methods for factorial design being implemented.
• Easier retrieving of genes, from free text input containing probe set and exemplar names or from BarleyBase BLAST top hits.
• Enhanced menu for accessing analysis and visualization functions.

01/29/04

•  NASCArrays, the Nottingham Arabidopsis Stock Centre's microarray database, generously agrees to share the Arabidopsis Affymetrix GeneChip data generated at their Affymetrix Facility with BarleyBase. Thanks to all people at NASC! We expect this will add over 40 experiments in 2004 to our repository for public access.

01/07/04

• BarleyBase is fully operational. Now it features a submission tool that is probably the least demanding on submitter's effort among microarray data submission tools, data visualization at different data levels, from hybridization to a single probe, and versatile feature (gene) filtering options. Full range of unsupervised analysis tools are provided too.
• BarleyBase has received three experiment submissions, which totals 104 Affymetrix GeneChips hybridizations. Thanks to all submitters!

12/01/03

• Data set management of filtered probe sets ( genes) and result management of analysis results. They enable easier comparison and combination of different filters and methods.

11/18/03

• Expression profile filters now allows user to define a subset of hybridizations from an experiment, and filter genes according to the expressions patterns of selected hybridizations .
• Browse probe sets from name lists, or search from probe sets using partial probe set name or exemplar name as input.

11/06/03

• Microarray data analysis capabilities are added as a TRIAL feature for BarleyBase. The analyses are available after running "Probe Set Query". Provided are standard statistical methods included in R and Bioconductor: Hierarchical Clustering, K-means and K-Medoids partitioning, Principal Component Analysis (PCA), Self-Organizing Maps (SOM) and Sammon's non-linear mapping

11/05/03

• Added search engine to BarleyBase, which can be accessed by typing keywords in the search bar on top of each page. It will quickly get users to their desired pages, and find all relevant information with one click.

11/04/03

• Plant Ontology is adapted at BarleyBase. Currently, Barley's Anatomy Ontology and Growth (Development) Stage Ontology from Gramene are included and accessible at "Sample Preparation" page.
• A tool for accessing and selecting the plant ontologies is added to the "Sample Preparation" page.

10/03

• Added MAGE-ML files generating capability for experiment submissions. Available for download.
• Added group management functionality under "My BarleyBase" menu.
• Updated exemplar sequence annotation based on BLASTX search against 270,000 plant protein sequences.
• Visualization of microarray data by scatter plots and M v A Plot  by hybridizations or by treatments means.

09/03

• BarleyExpress, our online experiment submission tool, is up to use.
• Download Center open to users.
• Added plotting functions for time-series style plot for a probe set, and the expression view plot for probe set neighbors.
• Added hierarchical clustering and k-means partition function to expression-profile filtered datasets.

09/19/03

• Dr. Rico Caldo from Roger Wise Lab submitted the first Barley1 GeneChip experiment to BarleyBase. This is the first experiment submission and is public to all users.

08/03

• Query for probe sets by expression profiles and by annotation were implemented.

6/08/03

• Affymetrix WebTalk: Dr. Tim Close, UC Riverside
  The Barley Microarray: An Example of Sharing and Cooperation.
  Wednesday, June 18, 2003
  9:00 a.m. PST, Seating will be limited, register now.
• Orders are now being accepted for the Barley GeneChip#174(Barley Genome Array); please contact Affymetrix for a quote. The part number for ordering is 511012 and arrays can be ordered in increments of five. The array will be available for shipment after June 28th.

• BLAST the Barley1 GeneChip in PlantGDB

• Barley1.CDF(Chip Description File for Barley1 GeneChip) is ready for downloading

• New BarleyBase team member Lishuang Shen started working as database administrator
• Set alias for BarleyBase website: http://barleybase.org
• Updated BarleyBase website by simplifying menu and combining schema, glossary, tools, people and help into DBOverview

For problems with the webpages, contact barleybasewebmaster