An "Electronic Fluorescent Pictograph" Browser for Exploring and Analyzing Large-scale Biological Data Sets

Overview

Journal PLoS One

Specialties General Medicine
Science

Date 2007 Aug 9

PMID 17684564

Citations 1259

Authors

Debbie Winter

Ben Vinegar

Hardeep Nahal

Ron Ammar

Greg V Wilson

Nicholas J Provart

Affiliations

Soon will be listed here.

Abstract

Background: The exploration of microarray data and data from other high-throughput projects for hypothesis generation has become a vital aspect of post-genomic research. For the non-bioinformatics specialist, however, many of the currently available tools provide overwhelming amounts of data that are presented in a non-intuitive way.

Methodology/principal Findings: In order to facilitate the interpretation and analysis of microarray data and data from other large-scale data sets, we have developed a tool, which we have dubbed the electronic Fluorescent Pictograph - or eFP - Browser, available at http://www.bar.utoronto.ca/, for exploring microarray and other data for hypothesis generation. This eFP Browser engine paints data from large-scale data sets onto pictographic representations of the experimental samples used to generate the data sets. We give examples of using the tool to present Arabidopsis gene expression data from the AtGenExpress Consortium (Arabidopsis eFP Browser), data for subcellular localization of Arabidopsis proteins (Cell eFP Browser), and mouse tissue atlas microarray data (Mouse eFP Browser).

Conclusions/significance: The eFP Browser software is easily adaptable to microarray or other large-scale data sets from any organism and thus should prove useful to a wide community for visualizing and interpreting these data sets for hypothesis generation.

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References

Sherlock G, Hernandez-Boussard T, Kasarskis A, Binkley G, Matese J, Dwight S . The Stanford Microarray Database. Nucleic Acids Res. 2000; 29(1):152-5. PMC: 29818. DOI: 10.1093/nar/29.1.152. View

Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O . The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 2007; 50(2):347-63. DOI: 10.1111/j.1365-313X.2007.03052.x. View

Lee S, Cheng H, King K, Wang W, He Y, Hussain A . Gibberellin regulates Arabidopsis seed germination via RGL2, a GAI/RGA-like gene whose expression is up-regulated following imbibition. Genes Dev. 2002; 16(5):646-58. PMC: 155355. DOI: 10.1101/gad.969002. View

Garcia-Hernandez M, Berardini T, Chen G, Crist D, Doyle A, Huala E . TAIR: a resource for integrated Arabidopsis data. Funct Integr Genomics. 2002; 2(6):239-53. DOI: 10.1007/s10142-002-0077-z. View

Rhee S, Beavis W, Berardini T, Chen G, Dixon D, Doyle A . The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res. 2003; 31(1):224-8. PMC: 165523. DOI: 10.1093/nar/gkg076. View

Mueller L, Zhang P, Rhee S . AraCyc: a biochemical pathway database for Arabidopsis. Plant Physiol. 2003; 132(2):453-60. PMC: 166988. DOI: 10.1104/pp.102.017236. View

Irizarry R, Hobbs B, Collin F, Beazer-Barclay Y, Antonellis K, Scherf U . Exploration, normalization, and summaries of high density oligonucleotide array probe level data. Biostatistics. 2003; 4(2):249-64. DOI: 10.1093/biostatistics/4.2.249. View

Birnbaum K, Shasha D, Wang J, Jung J, Lambert G, Galbraith D . A gene expression map of the Arabidopsis root. Science. 2003; 302(5652):1956-60. DOI: 10.1126/science.1090022. View

Craigon D, James N, Okyere J, Higgins J, Jotham J, May S . NASCArrays: a repository for microarray data generated by NASC's transcriptomics service. Nucleic Acids Res. 2003; 32(Database issue):D575-7. PMC: 308867. DOI: 10.1093/nar/gkh133. View

10.

Rocca-Serra P, Brazma A, Parkinson H, Sarkans U, Shojatalab M, Contrino S . ArrayExpress: a public database of gene expression data at EBI. C R Biol. 2004; 326(10-11):1075-8. DOI: 10.1016/j.crvi.2003.09.026. View

11.

Thimm O, Blasing O, Gibon Y, Nagel A, Meyer S, Kruger P . MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 2004; 37(6):914-39. DOI: 10.1111/j.1365-313x.2004.02016.x. View

12.

Yu H, Ito T, Zhao Y, Peng J, Kumar P, Meyerowitz E . Floral homeotic genes are targets of gibberellin signaling in flower development. Proc Natl Acad Sci U S A. 2004; 101(20):7827-32. PMC: 419691. DOI: 10.1073/pnas.0402377101. View

13.

Shin H, Shin H, Dewbre G, Harrison M . Phosphate transport in Arabidopsis: Pht1;1 and Pht1;4 play a major role in phosphate acquisition from both low- and high-phosphate environments. Plant J. 2004; 39(4):629-42. DOI: 10.1111/j.1365-313X.2004.02161.x. View

14.

Zimmermann P, Hirsch-Hoffmann M, Hennig L, Gruissem W . GENEVESTIGATOR. Arabidopsis microarray database and analysis toolbox. Plant Physiol. 2004; 136(1):2621-32. PMC: 523327. DOI: 10.1104/pp.104.046367. View

15.

Gilmour S, Zarka D, Stockinger E, Salazar M, Houghton J, Thomashow M . Low temperature regulation of the Arabidopsis CBF family of AP2 transcriptional activators as an early step in cold-induced COR gene expression. Plant J. 1999; 16(4):433-42. DOI: 10.1046/j.1365-313x.1998.00310.x. View

16.

Honys D, Twell D . Transcriptome analysis of haploid male gametophyte development in Arabidopsis. Genome Biol. 2004; 5(11):R85. PMC: 545776. DOI: 10.1186/gb-2004-5-11-r85. View

17.

Zhang W, Morris Q, Chang R, Shai O, Bakowski M, Mitsakakis N . The functional landscape of mouse gene expression. J Biol. 2004; 3(5):21. PMC: 549719. DOI: 10.1186/jbiol16. View

18.

Casson S, Spencer M, Walker K, Lindsey K . Laser capture microdissection for the analysis of gene expression during embryogenesis of Arabidopsis. Plant J. 2005; 42(1):111-23. DOI: 10.1111/j.1365-313X.2005.02355.x. View

19.

Schmid M, Davison T, Henz S, Pape U, Demar M, Vingron M . A gene expression map of Arabidopsis thaliana development. Nat Genet. 2005; 37(5):501-6. DOI: 10.1038/ng1543. View

20.

Toufighi K, Brady S, Austin R, Ly E, Provart N . The Botany Array Resource: e-Northerns, Expression Angling, and promoter analyses. Plant J. 2005; 43(1):153-63. DOI: 10.1111/j.1365-313X.2005.02437.x. View