2010 Jul

• Readymade & persistent GeneLists for public access:
  Now we have 18 persistent genelists available to all users. You can try these readymade lists 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

• Now 200 Publicly Accessible Experiments at PLEXdb:
  List of all public experiments
  
  • AraPLEX :19 Experiments from Arabidopsis
  • BarleyBase :44 Experiments from Barley
  • FusariumPLEX :12 Experiments from Fusarium
  • GrapePLEX :15 Experiments from Grape
  • MaizePLEX :19 Experiments from Maize
  • MedicagoPLEX :3 Experiments from Medicago
  • PoplarPLEX :10 Experiments from Poplar
  • RicePLEX :35 Experiments from Rice
  • SoyPLEX :16 Experiments from Soybean
  • SugarPLEX : 1 Experiment from Sugarcane
  • TomPLEX :3 Experiments from Tomato
  • WheatPLEX :21 Experiments from Wheat

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:
  
  
  Barley:
  • 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.
  
  Create:
  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.
  
  Analyze:
  Calculate fold-change, Hierarchical Clustering, Expression graph, Translate between Microarray Platforms, Heatmap, and Partitional Clustering.
  
  Annotate:
  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).'

2009/10/30

• 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.

2009/10/15

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

2009/09/15

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

2009/09/02

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

2009/08/13

• 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.
    

2009/07/24

• 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.
    

2009/03/31

• 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.

2009/01/22

• 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.

12/24/08

• 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.

11/19/08

• 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.

10/09/08

• 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.

09/17/08

• 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]

09/04/08

• 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.

08/25/08

• 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.

07/31/08

• 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

07/16/08

• 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

04/21/08

• 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.

03/24/08

• 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).

02/27/08

• 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).

2/21/08

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

1/2/08

• 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

11/13/07

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

10/24/07

• 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.

7/27/07

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

7/1/07

• 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.

6/27/07

• 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

6/22/07

• 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

10/31/06

• 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

9/15/06

• 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

07/10/06

• 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.