MapMan or related tools

  • Lohse M, Nagel A, Herter T, May P, Schroda M, Zrenner R, Tohge T, Fernie AR, Stitt M, Usadel B. (2013) Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data. Plant, cell & environment. 2013 Nov 15. doi: 10.1111/pce.12231. cited 3 times
  • Lohse M, Bolger A, Nagel A, Fernie A, Lunn J, Stitt M, Usadel B (2012)  Robina: A user-friendly, integrated software solution for RNA-Seq based transcriptomics. Nucleic Acids Research, 40:W622-7 cited 107 times
  • Lohse M, Nunes-Nesi A, Krueger P, Nagel A, Hannemann J, Giorgi FM, Childs L, Osorio S, Walther D, Selbig J, Sreenivasulu N, Stitt M, Fernie AR, Usadel B (2010) Robin: An intuitive wizard application for R-based expression microarray quality assessment and analysis, Plant Physiol., 153:642–651 cited 56 times
  • Usadel B, Poree F, Nagel A, Lohse M, Czedik-Eysenberg A, Stitt M (2009) A guide to using MapMan to visualize and compare Omics data in plants: a case study in the crop species, Maize. Plance Cell Environment  32:1211-1229 cited 87 times
  • Hannemann J, Poorter H, Usadel B, Bläsing OE, Finck A, Tardieu F, Atkin O, Pons T, Stitt  M, Gibon Y (2009) Xeml Lab: a software suite for a standardised description of the growth environment of  plants. Plant Cell Environment, 32:1185-1200 cited 9 times
  • Usadel B, Nagel A, Steinhauser D, Gibon Y, Blaesing OE, Redestig H, Sreenivasulu N, Krall L, Hannah MA, Poree F, Fernie AR, Stitt M (2006) PageMan an interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments, BMC Bioinformatics 18:7:535 cited 128 times
  • Usadel B, Nagel A, Thimm O, Redestig H, Bläsing OE, Palacios-Rojas N, Selbig J, Hannemann J, Piques MC, Steinhauser D, Scheible WR, Gibon Y, Morcuende R, Weicht D, Meyer S, Stitt M (2005) Extension of the Visualization Tool MapMan to Allow Statistical Analysis of Arrays, Display of Coresponding Genes, and Comparison with Known Responses. Plant Physiology, 138:1195-1204. cited 257 times
  • Thimm O, Bläsing O, Gibon Y, Nagel A, Meyer S, Krüger P, Selbig J, Müller LA, Rhee SY, Stitt M (2004) MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. Plant J. 37:914-39 cited 900 times


Adaptations of MapMan or its ontology

  • Rotter A, Camps C, Lohse M, Kappel C, Pilati S, Hren M, Stitt M, Coutos-Thévenot P, Moser C, Usadel B, Delrot S, Gruden K. (2009) Gene expression profiling in susceptible interaction of grapevine with its fungal pathogen Eutypa lata: extending MapMan ontology for grapevine. BMC Plant Biol. 9:104. cited 19 times
  • Howell K, Narsai R, Carroll A, Ivanova A, Lohse M, Usadel B, Millar AH, Whelan J(2009) Mapping metabolic and transcript temporal switches during germination in Oryza sativa highlights specific transcription factors and the role of RNA instability in the germination process. Plant Physiology 149:961-80  cited 42 times
  • May P, Wienkoop S, Kempa S, Usadel B, Christian N, Rupprecht J, Weiss J, Recuenco-Munoz L, Ebenhöh O, Weckwerth W, Walther D (2008) Metabolomics- and proteomics-assisted genome annotation and analysis of the draft metabolic network of Chlamydomonas reinhardtii. Genetics. 179:157-66.  cited 51 times
  • Sreenivasulu N, Usadel B,Winter A, Radchuk V, Scholz U, Stein N, Weschke W, Strickert M, Close TJ, Stitt M, Graner A, Wobus U (2008) Barley grain maturation and germination: Metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools. Plant Physiol., 146:1734-1761 cited 72 times
  • Rotter A, Usadel B, Baebler S, Stitt M, Gruden K (2007) Adaptation of the MapMan ontology to biotic stress responses: application in solanaceous species. Plant Methods. 3:10 cited 15 times
  • Tellstrom V, Usadel B, Thimm O, Stitt M, Kuster H, Niehaus K (2007) The Lipopolysaccharide of Sinorhizobium meliloti Suppresses defense-associated Gene Expression in Cell Cultures of the Host Plant Medicago truncatula. Plant Physiol. 143:825-37.  cited 50 times
  • Urbanczyk-Wochniak E, Usadel B,Thimm O, Nunes-Nesi A, Carrari F,  Davy M, Blaesing OE,  Kowalczyk M, Weicht D, Polinceusz A, Meyer S, Stitt M, Fernie AR (2006) Conversion of MapMan to allow the analysis of transcript data from Solanaceous species: effects of genetic and environmental alterations in energy metabolism in the leaf. Plant Molecular Biology, 60:773-92.  cited 66 times

Use cases of MapMan or its ontology

  • Wang H, Schauer N, Usadel B, Frassea P, Zouinea M, Hernould M, Latché A, Pecha J-C, Fernie AR, Bouzayen M (2009) Regulatory Features Underlying Pollination-dependent and independent Tomato Fruit Set Revealed by Transcript and Primary Metabolite Profiling. Plant Cell 21:1428-52 
  • Pauwels L, Morreel K, De Witte E, Lammertyn F, Van Montagu M, Boerjan W, Inzé D, Goossens A (2008) Mapping methyl jasmonate-mediated transcriptional reprogramming of metabolism and cell cycle progression in cultured Arabidopsis cells. PNAS 105:1380-5.  
  • Doehlemann G, Wahl R, Horst RJ, Voll LM, Usadel B, Poree F, Stitt M, Pons-Kühnemann J, Sonnewald U, Kahmann R, Kämper J.(2008) Reprogramming a maize plant: transcriptional and metabolic changes induced by the fungal biotroph Ustilago maydis. Plant J. 56:181-95.
  • Morcuende R, Bari R, Gibon Y, Zheng W, Datt Pant B, Blaesing O, Usadel B, Czechowski T,  Udvardi MK, Stitt M, Scheible WR (2007) Genome-wide reprogramming of metabolism and regulatory networks of Arabidopsis in response to phosphorus. Plant Cell Environment, 30:85-112.
  • Deeken R, Engelmann JC, Efetova M, Czirjak T, Müller T, Kaiser WM, Tietz O, Krischke M, Mueller MJ, Palme K, Dandekar T, Hedrich R (2006) An integrated view of gene expression and solute profiles of Arabidopsis tumors: a genome-wide approach. Plant Cell. 18:3617-34. 
  • Carrai F, Baxter C, Urbanczyk-Wochniak E, Zanor MI, Nunes-Nesi A, Usadel B, Nikiforova V, Centero D, Ratzka A, Pauly M, Sweetlove L, Fernie AR (2006) Integrated analysis of metabolite and transcript levels reveals tight co-ordinate regulation of metabolism underlies tomato fruit development. Plant Physiol, 142:1380-96
  • Osuna D, Usadel B, Morcuende R, Gibon Y, Blasing OE, Hohne M, Gunter M, Kamlage B, Trethewey R, Scheible WR, Stitt M (2006) Temporal responses of transcripts, enzyme activities and metabolites after adding sucrose to carbon-deprived Arabidopsis seedlings. Plant J., 49:463-91.
  • Gibon Y, Usadel B, Blaesing OE, Kamlage B, Hoehne M, Trethewey R, Stitt M (2006) Integration of metabolite with transcript and enzyme activity profiling during diurnal cycles in Arabidopsis rosettes. Genome Biol., 7:R76.
  •  Blaesing OE, Gibon Y, Guenther M, Hoehne M, Morcuende R, Thimm O, Usadel B, Scheible W-R, Stitt M (2005) Sugars and Circadian Regulation make Major Contributions to the Global Regulation of Diurnal Gene Expression in Arabidopsis. Plant Cell, 17:3257-3281.