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PLEXdb/BarleyBase News Archive

2011 News were published in Facebook

2011 Feb

2011 Jan

  • PLEXdb Demo and Poster at PAG XIX (San Diego, Jan-15 to Jan-19, 2011):
    PLEXdb will give a computer demo, present a poster and participate in the Consortium of PLant Genome Databases at the Plant & Animal Genomes XIX Conference, January 15-19, 2011, San Diego, CA. Below are the details on how to find us.
    • Computer Demo:
      Sunday - Late Afternoon, January 16, 2011, 4:50 pm
      PLEXdb: the Plant and Plant Pathogen Expression Resource for Functional Genomics
      (Computer Room, located in the California Room)
    • Poster: C893 ( Abstract)
    • Find us at Booth 427 in the Exhibit Hall (Plant Genome DB Outreach Consortium)
    • PLEXdb Now has Cotton Data Sets:
      The two cotton experiments at GEO have now been imported to PLEXdb. Please click here to see a page listing both these experiments.
      Please visit CottonPLEX, the expression resource page for Cotton.

    2010 Dec

    • New Data Sets for Tomato at TomPLEX:
      We have very recently added 9 tomato experiments to our collection, making it 12 publicly visible data sets. See a listing of all the publicly visible tomato experiments here.

      Tomato researchers may also want to visit our TomPLEX page for the expression resources for Tomato.

    2010 Nov

    • New Atlas Experiment for Tomato:
      Expression data from various tomato plant tissues.
      This is the latest experiment in our collection of expression atlases and it comes from Koh Aoki's lab in Kazusa DNA Research Institute, Chiba, Japan.
      The associated publication is:
      Ozaki S, Ogata Y, Suda K, Kurabayashi A, Suzuki T, Yamamoto N, Iijima Y, Tsugane T, Fujii T, Konishi C, Inai S, Bunsupa S, Yamazaki M, Shibata D, Aoki K. Coexpression analysis of tomato genes and experimental verification of coordinated expression of genes found in a functionally enriched coexpression module. DNA Res. 2010;17(2):105-16.

    2010 Oct

    • Some PLEXdb Statistics:
      • PLEXdb Crossed the 8000 Hybridizations Mark (300 data sets): Now PLEXdb houses expression data from more than 8000 hybridizations representing over 300 data sets.
      • Close to 6000 hybridizations are publicly visible (250 data sets).
      • Users have downloaded data from PLEXdb more than 26000 times since 2003.
      • Already downloaded 15000 times in 2010.
      • Total number of registered users: More than 1600.
      • A steady increase in new users: 240 added in 2007, 250 more in 2008, 300 in 2009 and already 230 in 2010.

    2010 Aug-Sep

    • Pathogenicity Related Experiments in Arabidopsis:
      We have been importing Arabidopsis experiments from GEO related to pathogenicity, insects and nematodes. Please scan the titles in the dropdown list at Browse AraPLEX Experiment Data page to choose these recent imports, now more than 35 and increasing.
      A Few Examples:
      • AT46 : Targets of AtWRKY27 in Arabidopsis leaves.
      • AT63 : Silverleaf whitefly 2nd instar feeding on 7-week old Arabidopsis thaliana rosette leaves.
      • AT64 : Expression profiling of A. thaliana wild type Columbia-0 and mutant gh3.5-1D in response to pathogen Pst DC3000(avrRpt2).
      • AT80 : Laser microdissection of Arabidopsis cells at the powdery mildew infection site.
      • AT83 : Arabidopsis thaliana gene expression changes upon treatment with green peach aphid saliva.
      • AT99 : Comparison between NuGEN's WT-Ovation Pico and One-Direct Amplification Systems(Nematode Infestation).

    2010 Jul

    • Readymade & persistent GeneLists for public access:
      Now we have 18 persistent genelists available to all users. You can try these readymade lists(prefixed with the word 'Example:') with various tools within our Genelist Suite. These genelists are based on the atlas experiments and are specific to one of the treatments as indicated from the title of the genelist.Two lists have been prepared per species where atlas experiments are available (The GeneList tool).

    • Recently Released Experiments:
      • ZM28 :"Circadian clock-mediated transcriptional regulation in maize" submitted from Frank G. Harmon's lab(Plant Gene Expression Center) at UC, Berkley.

      • BB62 :"Barley host response to the direct application of the trichothecene mycotoxin deoxynivalenol" submitted by Stephanie A. Gardiner from Gary J. Muehlbauer's lab(University of Minnesota). The supporting publication is: 'Transcriptome analysis of the barley-deoxynivalenol interaction: evidence for a role of glutathione in deoxynivalenol detoxification'; Gardiner, S.A., J. Boddu, F. Berthiller, C. Hametner, R. Stupar, G. Adam, and G.J. Muehlbauer. Mol. Plant-Microbe Interact. 23(7):962-976(2010).

    2010 Jun

    2010 May

    • Recently Released Experiments:
      • FG16 :Fusarium graminearum gene expression in wheat stems during infection. An experiment submitted by Heather E Hallen from Frances Trail's Lab at Michigan State University. This data set supports their publication: Triacylglyceride metabolism by Fusarium graminearum during colonization and sexual development on wheat. Guenther, John C, Hallen-Adams, Heather E, Buecking, H, Shachar-Hill, Y, and Trail, F. Mol Plant Microbe Interact. 22(12):1492-503(2009).

      • BB93 :Over-expression of ODDSOC2 in Golden Promise. Submitted by Aaron G Greenup from Ben Trevaskis group at CSIRO/ANU. The associated publication is: ODDSOC2 is a MADS box floral repressor that is down-regulated by vernalization in temperate cereals. Aaron G. Greenup, Shahryar Sasani, Sandra N. Oliver, Mark J. Talbot, Elizabeth S. Dennis, Megan N. Hemming and Ben Trevaskis. Plant Physiol. 2010 Apr 29. [Epub ahead of print].

    2010 Apr

    • A New and Large Expression Atlas in Rice:
      OS32: Dissecting the developmental transcriptomes of rice.

    • More Experiments Released at PLEXdb:

      • BB61: Transcriptome analysis of wild barley (H. vulgare ssp spontaneum) after pathogen inoculation. A Ben Millett submitted experiment from Gary Muehlbauer's lab in University of Minnesota. Associated publication: Wild barley expresses distinct sets of genes in response to pathogens of different trophic lifestyles. Millett, B.P et al. in Physiol. & Mol. Plant Path. (2009)

      • Grape:
      • VV16: Grape skin transcriptome in the berries grown on the vine treated with exogenous abscisic acid. An experiment submitted by Kazuya Koyama from the National Research Institute of Brewing. The data is associated with their publication in the Functional and Integrative Genomics' (2009 Oct 17 [Epub ahead of print])
      • VV17: Grape skin transcriptome in the berries cultured in vitro treated with exogenous abscisic acid. Another experiment from Kazuya Koyama of the National Research Institute of Brewing and supprts the same publication as VV16 above.

      • Wheat:
      • TA33: Wild emmer wheat comarison of drought resistant vs. susceptible genotypes under terminal drought. An experiment submitted by Krugman Tamar from Fahima Tzion's lab in Israel and it supports their publication:
        Multilevel regulation and signalling processes associated with adaptation to terminal drought in wild emmer wheat. Functional and Integrative Genomics. 2010.

    2010 Mar

    • Gene Expression Atlases at PLEXdb:
      Explore gene expression in diverse organs, tissues, or developmental stages.
      We have now 23 atlas experiments from 9 plant species:
      Arabidopsis, Barley, Maize, Medicago, Poplar, Rice, Soybean, Grape and Wheat.

    • PLEXdb Crossed the 5K Mark:
      Data from more than 5000 gene chips now for public access.

    2010 Feb

    • Fusarium Experiments at PLEXdb:

      PLEXdb is the only database that houses experiments based on the Fusarium Affymetrix chip. We have now 11 public microarray data sets from the Fusarium community.

      Two recently added experiments from John Manners' lab (CSIRO, Australia):

      • FG12 : Fusarium graminearum gene expression during crown rot of wheat.

      • FG14 :DON induction media. This expt. supports their publication, 'Novel Genes of Fusarium graminearum That Negatively Regulate Deoxynivalenol Production and Virulence', D. M. Gardiner, K. Kazan, and J. M. Manners. Mol Plant Microbe Interact. 2009 Dec;22(12):1588-600..

    2010 Jan

    • The Gene List Suite at PLEXdb

      A very useful collection of tools to create, analyze and annotate lists of genes.

      Import your own genelist, Combine genelists (Venn Diagram), Translate between microarrays, Fold change between any two treatments in an experiment, Profile Neighbors (Co-expressed genes), GO Category, Treatment-specific expressed genes, Blast against array sequence, and Translate to probe sets.

      Calculate fold-change, Hierarchical Clustering, Expression graph, Translate between Microarray Platforms, Heatmap, and Partitional Clustering.

      GO Annotation, Genbank Protein Accessions, UniProt IDs, Arabidopsis Loci, Rice Loci, NCBI RefSeq, TIGR Transcript Assemblies, DCFI GeneIndex, Consensus Sequence, KEGG, Manufacturer Annotation, Community Annotation, and Grape Genome.

    2009 Dec

    • Gene OscilloScope ver-2 for multiple genes, a data mining tool:

      Search for experiments where your favorite genes show high fluctuation (oscillation) in their expression.

      If the expression of a probe set (gene) is affected by some of the treatments in an experiment, it shows a higher CV (more fluctuation); if the expression is less affected by the treatments, it shows a lower CV (minimal fluctuiation).

    • A Few More Experiments at PLEXdb:

      • TA24: Transcription profiling wheat responses to adapted and non-adapted isolates of the blast fungus, Magnaporthe. This data set has been submitted from Lesley Boyd's Lab at the John Innes Centre, U.K. and supports their publication:
        Wheat blast: histopathology and transcriptome reprogramming in response to adapted and nonadapted Magnaporthe isolates. Tufan HA et al. New Phytologist 184(2):473-484 (2009).

      • BB73: Comparative transcriptional profiling of organs of the barley spike.
        This experiment from Tilahun Abebe's lab(University of Northern Iowa) has recently been made public and the result has appeared in:
        Comparative Transcriptional Profiling Established the Awn as the Major Photosynthetic Organ of the Barley Spike While the Lemma and the Palea Primarily Protect the Seed . Tilahun Abebe, Roger P. Wise, and Ronald W. Skadsen. Plant Genome 2:247-259 (2009)

      • BB76: Structural and functional characterization of a winter malting barley. This experiment is from Gary Muehlbauer's lab at Univ. of Minn.

      • BB89: Gene expression in the barley spike during drought stress. Another experiment from Tilahun Abebe's lab. Associated publication:
        Drought response in the spikes of barley: gene expression in the lemma, palea, awn, and seed. Tilahun Abebe1, Kalpalatha Melmaiee1, Virginia Berg and Roger P. Wise. Functional & Integrative Genomics (Nov 2009).

    2009 Nov

    • Poplar Expression Data Now at PLEXdb:

      PLEXdb has recently imported from GEO 6 experiments based on Poplar61k Affymetrix Genome Array.
      You can browse them at PoplarPLEX:

    • New Experiments Available at PLEXdb:

      • VV14 :A phytoplasma infection experiment in grape from Nicola Pecchioni's lab (University of Modena and Reggio Emilia, Italy). The data is associated with the following publication:
        Gene expression in grapevine cultivars in response to Bois Noir phytoplasma infection. Albertazzi G., Caffagni A., Milc J.A., Francia E., Roncaglia E., Ferrari F., Tagliafico E., Stefani E., Pecchioni N. Plant Science 176: 792-804 (2009). Submitted at GEO via PLEXdb.

      • BB46 : From Wise Lab, ISU. Comparison of wild-type and cell death mutant of barley plants containing Mla6 powdery mildew resistance gene. This data set has now generated two publications.
        'Transcript-Based Cloning of RRP46, a Regulator of rRNA Processing and R Gene-Independent Cell Death in Barley-Powdery Mildew Interactions. Xi L, Moscou MJ, Meng Y, Xu W, Caldo RA, Shaver M, Nettleton D, Wise RP. Plant Cell (2009 Oct 27)'. And,
        'Interaction-Dependent Gene Expression in Mla-Specified Response to Barley Powdery Mildew. Rico A. Caldo, Dan Nettleton and Roger P. Wise. Plant Cell 16:2514-2528 (2004).' Submitted at GEO via PLEXdb.

      • FG11 : Gene Regulation by Fusarium Transcription Factors Tri6 and Tri10. The data is associated with the same publication as FG10 below.

      • FG10 : Response to trichodiene treatment in Fusarium graminearum. This accession supports their publication: 'Global gene regulation by Fusarium transcription factors Tri6 and Tri10 reveals adaptations for toxin biosynthesis. Seong, K., Pasquali, M., Song, J., Hilburn, K., McCormick, S., Dong, Y., Xu, J.-R. and Kistler, H.C. Molecular Microbiology 72: 354-367 (2009).'

      • BB65 : Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants. The resulting publication is ' Transcriptome Analysis of Cold Acclimation in Barley Albina and Xantha Mutants. Jan T. Svensson, Cristina Crosatti, Chiara Campoli, Roberto Bassi, Antonio Michele Stanca, Timothy J. Close and Luigi Cattivelli. Plant Physiology 141:257–270(2006).'


    • A complement to PLEXdb:
      • A quote from a recent publication: New Phytol. 2009 Oct;184(2):473-84. Epub 2009 Jul 23. PubMed PMID: 19645735.
        "....Plexdb regularly updates probe set annotations through similarity searches to multiple publicly available databases ...."
        The publication is associated with the PLEXdb wheat accession TA24. In the article, look under Results in the first paragraph of subsection, 'Transcriptome profiling in wheat cv. Renan–Magnaporthe interactions' for this quote.


    • Barley data from NCBI-GEO:
      • Please visit 12 recently imported experiments from NCBI-GEO. Now PLEXdb has 40 barley experiments for public view.


    • Sugarcane:
      • Now we have sugarcane expression data at PLEXdb along with annotation support for the Sugar Cane 8k affymetrix genechip.


    • Wheat imports from NCBI-GEO:
      • PLEXdb has now 17 publicly visible wheat experiments including 6 recent imports from NCBI-GEO.


    • Soybean data from NCBI-GEO:
      • PLEXdb is now home to 13 more soybean data series imported from NCBI-GEO. Now we have 16 publicly visible experiments associated with the Soybean Affymetrix chip.


    • New Rice and Maize Experiments Imported from NCBI-GEO:
      • Rice : 22 experiments have recently been imported from GEO and are now part of a collection of 26 rice experiments publicly visible.

      • Maize : PLEXdb has added 16 experiments from GEO. Now there are 18 maize experiments visible to the public.


    • New Barley Experiments Released:
      • BB63 : Late response to boron toxicity in barley leaves. The associated publication is: Microarray Analysis of Late Response to Boron Toxicity in Barley (Hordeum vulgare L.) Leaves. Turkish Journal of Agriculture and Forestry, 33: 191-202, 2009.
        BB63 has also been submitted at GEO via PLEXdb, GSE14521.

      • BB20 : Genotype-dependent gene expression in barley. From Arnis Druka's group.

      • BB21 : Genetics of gene expression in barley. This data set supports two of their publications:
        'Gene expression quantitative trait locus analysis of 16000 barley genes reveals a complex pattern of genome-wide transcriptional regulation'. Potokina E, Druka A, Luo Z, Wise R, Waugh R, Kearsey M. The Plant Journal. 2007 Oct 18.
        'SFP Genotyping From Affymetrix Arrays Is Robust But Largely Detects Cis-acting Expression Regulators', Z. W. Luo, E. Potokina, A. Druka, R. Wise, R. Waugh and M. J. Kearsey Genetics, Vol. 176, 789-800, June 2007.


    • BB10: A Barley pathogenesis experiment on powdery mildew has been released from Roger Wise's group. This data set is associated with their publication: 'Blufensin1 negatively impacts Basal defense in response to barley powdery mildew'. Meng Y, Moscou MJ, Wise RP. 2009(Jan). Plant Physiol. 149(1):271-85.


    • Gene OscilloScope:   A new tool at PLEXdb to find out in which experiment your favorite gene does something interesting !
      Given a probe set, it searches for experiments where the expression of a queried gene fluctuates (oscillates) the most. The result displays the extent of fluctuation (CV) of the treatment means in each of the experiments visible to the user.


    • Medicago Gene Expression Atlas: ME1 from Michael Udvardi's lab is now in PLEXdb and is a useful addition to our other gene expression atlas experiments in wheat, barley and Arabidopsis. It supports the publication: A gene expression atlas of the model legume Medicago truncatula. Benedito VA, Torres-Jerez I, Murray JD, Andriankaja A, Allen S, Kakar K, Wandrey M, Verdier J, Zuber H, Ott T, Moreau S, Niebel A, Frickey T, Weiller G, He J, Dai X, Zhao PX, Tang Y, Udvardi MK. Plant J. 2008 Aug;55(3):504-13. Epub 2008 Apr 12.


    • Submission at GEO via PLEXdb: PLEXdb has already submitted 7 experiments at GEO on behalf of the original submitters: 3 of these are public and 4 are private at GEO. You are welcome to take advantage of this facility. Two birds in one shot: Submit your data once, at PLEXdb, and with your consent we deposit it at NCBI-GEO. You always have the choice to keep it private at GEO.

    • Annotation: Microarray annotation has been updated to TAIR 8 and the August, 2008 release of UniProt uniref90 sequence.


    • Expression Atlas of Arabidopsis Development (from AtGenExpress), AT40 can now be accessed at PLEXdb. The accession AT40 compares the expression of 63 tissues from wildtype Columbia. It's accompanying accession AT41 includes a few developmental mutants along with the corresponding WT controls.

    • AT31:A pathogenicity experiment in Arabdopsis has now been made publicly visible by Michael Krogh Jensen, University of Copenahgen. AT31 data set relates to their publication: Transcriptional regulation by a NAC (NAM-ATAF1,2-CUC2) transcription factor attenuates ABA signalling for efficient basal defence towards Blumeria graminis f.sp. hordei in Arabidopsis., Jensen MK, Hagedorn PH, de Torres-Zabala M, Grant MR, Rung JH, Collinge DB, Lyngkjaer MF. Plant J. 2008 Aug 6. [Epub ahead of print]


    • Two tools have been added to PLEXdb.
      • The Microarray Platform Translator (MPT) has been re-designed and re-implemented from its predecessor in BarleyBase.
      • The GO annotator retrieves GO annotation for one or more probe set ids.


    • TA3 - Wheat Gene Atlas released. Thirteen developmental stages from seed to seed: From Andreas Schreiber, Ute Baumann, Tim Sutton, Roger Wise, Gary Muehlbauer, Robbie Waugh and Peter Langridge.


    • A wheat P.s. tritici infection experiment, TA11 has now been released courtesy of Dr. TE Coram. This data supports their publication: Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction. TRISTAN E. CORAM, MATTHEW L. SETTLES AND XIANMING CHEN. MOLECULAR PLANT PATHOLOGY (2008) 9(4), 479-493


    • The 3.0 version of the Model Genome Interrogator has been released. Credits: Lu, H., N. Lauter, E. Cannon, S. Dash, D. Hessel, M. Moscou, R. Wise, J. Dickerson, V. Brendel


    • We are pleased to announce the release of our newest Affymetrix GeneChip page for cotton. PLEXdb now provides annotation information for cotton along with access to all of its statistical and visualization tools. We will be happy to receive your cotton GeneChip data as a common resource for the cotton and greater plant communities.


    • New Experiments Released:
      • BB49 : A 'Barley stem rust interaction' experiment from Dr. A. Kleinhofs. This data set supports the publication: Parallel expression profiling of barley�stem rust interactions. Zhang L, Castell-Miller C, Dahl S, Steffenson B, Kleinhofs A. Funct Integr Genomics (2008, Jan 15, epub ahead of print)

      • BB53 : Another Barley dat set, 'Functional Genomic Analysis Of Barley(Hordeum vulgare L.) Grain Protein Accumulation' and the corresponding publication is: Aravind K. Jukanti, Nancy M. Heidlebaugh, David L. Parrott, Isabelle A. Fischer, Kate McInnerney and Andreas M. Fischer. Comparative transcriptome profiling of near-isogenic barley (Hordeum vulgare) lines differing in the allelic state of a major grain protein content locus identifies genes with possible roles in leaf senescence and nitrogen reallocation. New Phytologist 177(2):333-349 (Jan 2008).


    • New Experiments Released:
      • GM3 : Expression patterns in time and space during P.sojae infection of soybean cultivars differing in quantitative resistance. A large soybean-pathogen dat set released from Brett Tyler(Bruno Sobral).

      • FG7 : Another Fusarium data set from Dr.Gary Muehlbauer: Fusarium gene expression profiles during conidia germination stages. Please see their publication: Seong KY, Zhao X, Xu JR, G�ldener U, Kistler HC. Conidial germination in the filamentous fungus Fusarium graminearum. Fungal Genetics and Biology (2007 Sep 14).

      • TA9 : The first wheat-pathogen experiment in PLEXdb, TA9, has been released from Dr. Xianming Chen's lab. This data set supports the publication: TRISTAN E. CORAM, MEINAN WANG AND XIANMING CHEN. Transcriptome analysis of the wheat�Puccinia striiformis f. sp. tritici interaction. MOLECULAR PLANT PATHOLOGY 9 (2): 157-169 (2008).


    • The PLEXdb Software Workshop presentation for PAG XVI, 2008 is now available as a PDF.


    • Soybean experiment GM2 released: 'Distinct biphasic mRNA changes in response to Asian soybean rust infection', van de Mortel M, Recknor JC, Graham MA, Nettleton D, Dittman JD, Nelson RT, Godoy CV, Abdelnoor RV, Almeida AM, Baum TJ, Whitham SA


    • Annotation for Rice Array long oligo 45k microarray completed. The new annotation page covers probes on both the 20k and 45k arrays.


    • PLEXdb 2.0 has been released. New features include:
      • new server with significantly more storage (Sun X4600 Server with 4 dual core CPU's and 16GB of memory and a Sun SE6140 disk array with 8TB of data storage).
      • PLEX Express, the new experiment submission process, and a revised normalization pipeline for processing expression data, which provides more visualizations and types of downloadable data.
      • updated database schema in keeping with MIAME/Plant recommendations.
      • new experiment navigation; all aspects of an experiment are accessible from one page.
      • all microarray annotation has been updated.


    • A new PLEXdb tool for retrieving an annotation table for a list of probesets has been released.


    • The new PLEXdb experiment processing pipeline has been completed. We have redesigned the experiment processing pipeline which runs RMA and MAS analysis on experiments after they have been finalized, generates a number of images and plots, and prepares files for download. The new pipeline is more rigorous and uses the latest analysis tools from Bioconductor and Affymetrix.


    • VV3 released: 'Tissue-specific mRNA expression profiling in grape berry tissues', Grimplet J, Deluc LG, Tillett RL, Wheatley MD, Schlauch KA, Cramer GR, Cushman JC, BMC Genomics. 2007 Jun 21;8(1):187


    • VV7 released: 'Gene expression associated with compatible viral diseases in grapevine cultivars', Espinoza C, Vega A, Medina C, Schlauch K, Cramer G, Arce-Johnson P, Funct Integr Genomics 2007 Apr;7(2):95-110. Epub 2006 Jun 15


    • Experiment BB28 released. This experiment corresponds to the publication, 'Rpr1, a gene required for Rpg1-dependent resistance to stem rust in barley'. L. Zhang, T. Fetch, J. Nirmala, D. Schmierer, R. Brueggeman, B. Steffenson and A. Kleinhofs


    • New publication of meta-analysis of barley-powdery mildew interactions: Caldo RA, D Nettleton, J Peng, and RP Wise. 2006. Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles. Molecular Plant-Microbe Interactions 19(9): 939-947. Supports accession BB4 and BB2


    • The publication 'Genetic diversity contribution to errors in short oligonucleotide microarray analysis', Kirst M, Caldo R, Casati P, Tanimoto G, Walbot V, Wise RP, and Buckler ES has been published in Plant Biotechnology Journal. The data set ZM1 is ovailable here.


    • 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.


    • The program, Download Sequence, is upgraded. Now it supports searching for the sequences of all probes for all species/GeneChips within PLEXdb.


    • 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.


    • 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.


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



    • 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.


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


    • 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.


    • 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.


    • 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.


    • The links of Maize Cornchip0 (8k) now work properly for both BarleyBase and Plexdb.


    • 'Download Sequences' (one of the tools) now works properly in Plexdb.


    • Rice Genome Mapper was updated again with more new features.


    • Porting BarleyBase tools to PLEXdb is mostly done, with updated annotation pages and data access flow.


    • Rice Genome Mapper now supports 4 microarray platforms: Barley1 22K, Maize 18K, Rice 57K and Wheat 61K GeneChips.


    • Plant Ontology browser support both Developmental Ontology and Structure ontology, as response to the Plant Ontology Consortium ( announcement of the first release of the Developmental Ontology for flowering plants.


    • The first two experiments for 16k Grape Vitis_vinifera GeneChip are added by Dr. Grant Cramer's group at University of Nevada.


    • 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.


    • 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.


    • The Maize Genome Array  contains 17,555 probe sets to interrogate approximately 14,850 Zea mays transcripts, which represent 13,339 genes.


    • Plant Ontology Browser added, with updated plant ontology information.


    • Updated plant structure ontology is added for annotating samples in BarleyExpress.


    • BarleyBase now supports 11 high-density plant and pathogen microarray platforms:
      1. 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.
      2. One Affymetrix Plant Pathogen Platform: Fusarium.
      3. Two Spotted Oligo Microarray Platforms: 58K Maize and 20K Rice.


    • 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.


    • 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.


    • Microarray Platform Translator is added for enhances comparative-genomics support. It functions to allow:
      1. Translate exemplar names between any platforms we have. Currently it support translation of 7 chips to Barley1 or ATH1
      2. Assign any GenBank names, Accession and GI numbers to same species microarray elements. Will support all platforms we have.
      3. Given microarray element identifiers, find updated sequence members for corresponding contigs .
      4. Assign any sequences to DIFFERENT/SAME species platforms.


    • 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.



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


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

      We now fully 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.


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


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


    • 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.


    • 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.


    • 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.


    • 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.


    • 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.



    • 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".


    • 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.


    • 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.


    • 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.


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


    • "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.


    • 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.


      • 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.



    • 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!


    • 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.


    • 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.


    • 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


    • 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.


    • 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.


    • 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.


    • 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.


    • 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.


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


    • 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:
    • Updated BarleyBase website by simplifying menu and combining schema, glossary, tools, people and help into DBOverview
  • Added "Feedback" form into BarleyBase website.


  • Updated the BarleyBase website.


  • Redesigned the Experiment Setup part of AADM schema according to MIAME standard.


  • Drew the AADM schema using ERwin 4.1 for redesigning the BarleyBase schema to MIAME-compliant


  • Dr.Dickerson gave a presentation at weekly MicroArray group meeting, see slides here




  • 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



  • Downloaded the BASE
  • Uploaded *.CEL files into BASE



  • .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



  • 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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