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PLEXdb/BarleyBase News Archive
04/06/06
- Another Barley1 data set, BB3, contributed by Robbie Waugh.
This dataset supports the
publication: Arnis Druka, Gary Muehlbauer, Ilze Druka, Rico Caldo,
Ute Baumann, Nils Rostoks, Andreas Schreiber, Roger Wise, Timothy
Close, Andris Kleinhofs, Patrick Hayes, Jim McNicol, David Marshall,
and Robbie Waugh, 'An atlas of gene expression from seed to seed
through barley development',
Functional & Integrative Genomics, DOI 10.1007/s10142-006-0025-4.
04/06/06
- The program, Download Sequence, is upgraded. Now it supports
searching for the
sequences of all probes for all species/GeneChips within PLEXdb.
04/03/06
- A new Barley-Fusarium data set was released from Dr.Gary
Muehlbauer. The PLEXdb accession number is BB9. This dataset
supports the publication: Boddu, S.
Cho, W. M. Kruger, and G. J. Muehlbauer,
Transcriptome Analysis of the Barley-Fusarium graminearum
Interaction,
Molecular Plant Microbe Interactions, Vol. 19,
No. 4, 2006, pp. 407-417.
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
02/17/06
02/06/06
- Exemplar annotation and Probe alignment for Affymetrix Poplar
Genome Array (Populus sp 61K) are available.
01/16/06
- Annotations for species were updated.
01/16/06
- The tools: Data Access->Experiments->Hybridizations/Visualization
were updated. Scatter plot tool is available.
01/16/06
- The tool: Data Access->Genelists->Analysis is available.
01/16/06
- 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.
12/06/05
- Exemplar annotation and Probe alignment for Affymetrix
61K Medicago Genome Array (M. truncatula 50.9K,
M. sativa 1.9K, S. meliloti 8.3K) are added.
11/16/05
- The links of Maize Cornchip0 (8k) now work properly for
both BarleyBase and Plexdb.
11/16/05
- 'Download Sequences' (one of the tools) now works properly in Plexdb.
11/16/05
- Rice Genome Mapper was updated again with more new features.
08/11/05
- Porting BarleyBase tools to PLEXdb is mostly done, with
updated annotation pages and data access flow.
08/11/05
- Rice Genome Mapper now supports 4 microarray platforms:
Barley1 22K, Maize 18K, Rice 57K and Wheat 61K GeneChips.
08/11/05
- Plant Ontology browser support both Developmental Ontology
and Structure ontology, as response to the Plant Ontology Consortium
(www.plantontology.org) announcement of the first release of the
Developmental Ontology for flowering plants.
08/10/05
- The first two experiments for 16k Grape Vitis_vinifera
GeneChip are added by Dr.
Grant Cramer's group at University of Nevada.
07/06/05
- Exemplar annotation and Probe alignment and support for
Affymetrix 8K Sugar Cane Genome Array are added. The
Sugar Cane Genome Array contains over 8200 probe sets to
interrogate approximately ~7,500 sugar cane transcripts, including
4,447 sugar cane UniGene Clusters.
02/22/05
- Exemplar annotation and Probe alignment and support for
Affymetrix 18K Maize Genome Array are added. Now we support 3 maize
microarray platforms: Affymetrix 18K and 8K
array and long oligo 58K array.
02/22/05
- The
Maize Genome Array contains 17,555 probe sets to interrogate
approximately 14,850 Zea mays transcripts, which represent
13,339 genes.
02/14/05
- Plant Ontology Browser added, with updated plant ontology
information.
02/14/05
- Updated plant structure ontology is added for annotating samples in
BarleyExpress.
02/14/05
- BarleyBase now supports 11 high-density plant and pathogen microarray
platforms:
- Eight Affymetrix Plant Platforms: Arabidopsis: 8K AG and
22K ATH1; Barley: 22K Barley1; Maize: 8K CornChip0; Rice: 57K; Grape:
16K; Soybean: 61K with pathogens; Wheat: 61K.
- One Affymetrix Plant Pathogen Platform: Fusarium.
- Two Spotted Oligo Microarray Platforms: 58K Maize and 20K Rice.
02/14/05
- Exemplar
annotation for 58K Maize Spotted Oligo Microarray is added. Data
from this array can be submitted to BarleyBase for cross reference
to expression data from orthologous genes in other species.
This is developed by the NSF
Maize Oligonucleotide Array Project. It contains ~57k maize
50-70mer oligonucleotides, with the majority of these sequences
obtained from the TIGR
Maize Gene Index (Release 13.0) with additional sequences obtained
from the Consortium for
Maize Genomics, the PLANT and dbEST divisions of GenBank and
individual investigators.
01/26/05
- Exemplar
annotation for 20k Rice Spotted Oligo Microarray is added. Data
from this array can be submitted to BarleyBase for cross reference
to expression data from orthologous genes in other species.
This is the "Rice oligo version 2" developed by the
NSF Rice Oligonucleotide Array
Project. It contains 20,230 oligonucleotides which were
designed using gene models from
the TIGR Rice Annotation Database that have EST and/or full-length
cDNA support. The oligos were cross referenced to the
KOME full-length cDNA
dataset.
01/16/05
- Microarray Platform Translator is added for enhances
comparative-genomics support. It functions to allow:
- Translate exemplar names between any platforms we have. Currently
it support translation of 7 chips to Barley1 or ATH1
- Assign any GenBank names, Accession and GI numbers to same
species microarray elements. Will support all platforms we have.
- Given microarray element identifiers, find updated sequence members
for corresponding contigs .
- Assign any sequences to DIFFERENT/SAME species platforms.
01/10/05
- Exemplar annotation and Probe alignment for Affymetrix 57k Rice
GeneChip are added.
We now support the 57k Rice GeneChip. The
Rice Genome Array contains probe sets to detect transcripts from
all the high-quality expressed sequence from the entire rice genome
which includes 51,279 transcripts representing two rice cultivars.
The Rice Genome Array contains approximately 48,564 japonica
transcripts and 1,260 transcripts representing the indica
cultivar.
12/20/04
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
12/01/04
11/29/04
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 Arrayincudes 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
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 experiment 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.
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
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.
6/03/03
6/02/03
- Barley1.CDF(Chip Description File for Barley1
GeneChip) is ready for downloading
5/05/03
- 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
4/20/03
- Added "Feedback" form into BarleyBase website.
1/21/03
- Updated the BarleyBase website.
11/08/02
- Redesigned the Experiment Setup part of AADM schema
according to MIAME standard.
11/06/02
- Drew the AADM schema using ERwin 4.1 for redesigning
the BarleyBase schema to MIAME-compliant
10/23/02
- Dr.Dickerson gave a presentation at weekly MicroArray
group meeting, see slides
here
10/9/02
9/18/02
- Finished the mapping between the AADM schema and
Affymetrix data
- Downloaded Dchip, and used it to analyze the Affy
data
- Finished the mapping between MIAME and Affymetrix
experiment information
8/26/02
- Downloaded the BASE
- Uploaded *.CEL files into BASE
8/12/02
- .CEL files were loaded into table spot_result, and
the following fields were filled: x, y, intensity, sd,
pixels
- .TXT/.EXL files were loaded into table
abs_gene_expr_result, and the following fields were
filled: number_positive, number_negative, number_all,
number_used, number_in_avg, avg_diff_intensity
7/24/02
- BarleyBase database, which is on the server vracs001,
was bulit
- BarleyBase structure was finished, referring to
Affymetrix AADM schema
- Partial tables of barleybase were filled with
arabidopsis data(AtGenome1) downloaded from
Affymetrix
- The following columns were added into the table
scheme_unit:
- genbank_no
- description
- sequence
- start_position
- end_position
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