PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

By Björn Usadel, Axel Nagel, D. Steinhauser, Y. Gibon, O. Bläsing, Henning Redestig, N. Sreenivasulu, L. Krall, M. Hannah, F. Poree and 2 more. BMC Bioinformatics, 2006

360 citations recorded by the source corpus.

BackgroundMicroarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis.ResultsHere we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs.PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis.PageMan offers a complete user's guide, a web-based over-representation analysis as well as a tutorial, and is freely available at http://mapman.mpimp-golm.mpg.de/pageman/.ConclusionPageMan allows multiple microarray experiments to be efficiently condensed into a single page graphical display. The flexible interface allows data to be quickly and easily visualized, facilitating comparisons within experiments and to published experiments, thus enabling researchers to gain a rapid overview of the biological responses in the experiments.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/b27c02de4af28736526ec147d783a0f736aebb79

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Citations in the corpus

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists (2008, neutral): “Tools, such as GOBar (32), Go-Mapper (22), GOAlie, PageMan (51), high-throughput GoMiner (39), and the most recent, GOEAST (70), are intended to provide some of these capabilities to display multiple time course datasets simultaneously.”
KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases (2011, background): “A growing number of tools have been developed for pathway and disease identiﬁcation, including, but not limited to, MAPPFinder (13), EASE (14), DAVID (15,16), ArrayXPath (17), WebGestalt (18), FuncCluster (19), PageMan (20), GENECODIS (21,22), GeneTrail (23), g:Proﬁler (24), FunNet (25) and PaLS (26”
Three Arabidopsis SnRK2 protein kinases, SRK2D/SnRK2.2, SRK2E/SnRK2.6/OST1 and SRK2I/SnRK2.3, involved in ABA signaling are essential for the control of seed development and dormancy. (2009, methodology): “Using the Arabidopsis gene ontology database and analysis tool of PageMan (http://mapman.mpimp-golm.mpg.de/index.shtml; Usadel et al. 2006), we obtained ontological profiles of the top 100 down- and up-regulated genes in seeds of the srk2d/e/i mutant.”
Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. (2014, methodology): “, 2012) and tools for visualization of transcriptome responses, statistical analysis and cross-species pathway analysis (Thimm et al. 2004; Usadel et al. 2006; 2009).”
ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana (2011, neutral): “The cDNA was cloned via added PmeI/PacI sites into a modified pGreen0229-35S plant transformation vector (Skirycz et al., 2006).”
ToppCluster: a multiple gene list feature analyzer for comparative enrichment clustering and network-based dissection of biological systems (2010, background): “PageMan (11) is an innovative application that allows analysis of multiple microarray expression proﬁle clusters at a time, with an intuitive heatmap visualization based on set enrichments to organism-speciﬁc user-generated ontology mapping ﬁles.”