Literature DB >> 23913834

Data visualization in environmental proteomics.

Henry Mehlan1, Frank Schmidt, Stefan Weiss, Julia Schüler, Stephan Fuchs, Katharina Riedel, Jörg Bernhardt.   

Abstract

From raw data to gene expression profiles, from single cultures to complex microbial communities, environmental proteomics works with data of different complexity levels that need to be interpreted in detail or in its entirety. Although data visualization is closely connected with data analysis approaches, this work will solely focus on data visualization. Complementing traditional tools such as bar charts or line graphs, scientists and visualization professionals have been provided sophisticated visualization tools. Many rules and concerns regarding the display of single but also complex data will be reviewed and discussed. Visual approaches such as microcharts, heat maps, stream graphs, and tree maps will be brought to the reader's attention and demonstrated by utilizing real data sets.
© 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Keywords:  Data visualization; Environmental proteomics; Stream graphs; Technology; Tree maps

Mesh:

Substances:

Year:  2013        PMID: 23913834     DOI: 10.1002/pmic.201300167

Source DB:  PubMed          Journal:  Proteomics        ISSN: 1615-9853            Impact factor:   3.984


  10 in total

1.  A complete and flexible workflow for metaproteomics data analysis based on MetaProteomeAnalyzer and Prophane.

Authors:  Henning Schiebenhoefer; Kay Schallert; Bernhard Y Renard; Kathrin Trappe; Emanuel Schmid; Dirk Benndorf; Katharina Riedel; Thilo Muth; Stephan Fuchs
Journal:  Nat Protoc       Date:  2020-08-28       Impact factor: 13.491

2.  Proteomic analysis of carbon concentrating chemolithotrophic bacteria Serratia sp. for sequestration of carbon dioxide.

Authors:  Randhir K Bharti; Shaili Srivastava; Indu Shekhar Thakur
Journal:  PLoS One       Date:  2014-03-11       Impact factor: 3.240

3.  Fur is the master regulator of the extraintestinal pathogenic Escherichia coli response to serum.

Authors:  Sagi Huja; Yaara Oren; Dvora Biran; Susann Meyer; Ulrich Dobrindt; Joerg Bernhard; Doerte Becher; Michael Hecker; Rotem Sorek; Eliora Z Ron
Journal:  mBio       Date:  2014-08-12       Impact factor: 7.867

Review 4.  Open source libraries and frameworks for biological data visualisation: a guide for developers.

Authors:  Rui Wang; Yasset Perez-Riverol; Henning Hermjakob; Juan Antonio Vizcaíno
Journal:  Proteomics       Date:  2015-02-05       Impact factor: 3.984

5.  Impact of Dietary Resistant Starch on the Human Gut Microbiome, Metaproteome, and Metabolome.

Authors:  Tanja V Maier; Marianna Lucio; Lang Ho Lee; Nathan C VerBerkmoes; Colin J Brislawn; Jörg Bernhardt; Regina Lamendella; Jason E McDermott; Nathalie Bergeron; Silke S Heinzmann; James T Morton; Antonio González; Gail Ackermann; Rob Knight; Katharina Riedel; Ronald M Krauss; Philippe Schmitt-Kopplin; Janet K Jansson
Journal:  MBio       Date:  2017-10-17       Impact factor: 7.867

6.  The AGXX® Antimicrobial Coating Causes a Thiol-Specific Oxidative Stress Response and Protein S-bacillithiolation in Staphylococcus aureus.

Authors:  Vu Van Loi; Tobias Busche; Thalia Preuß; Jörn Kalinowski; Jörg Bernhardt; Haike Antelmann
Journal:  Front Microbiol       Date:  2018-12-11       Impact factor: 5.640

7.  Redox-Sensing Under Hypochlorite Stress and Infection Conditions by the Rrf2-Family Repressor HypR in Staphylococcus aureus.

Authors:  Vu Van Loi; Tobias Busche; Karsten Tedin; Jörg Bernhardt; Jan Wollenhaupt; Nguyen Thi Thu Huyen; Christoph Weise; Jörn Kalinowski; Markus C Wahl; Marcus Fulde; Haike Antelmann
Journal:  Antioxid Redox Signal       Date:  2018-01-30       Impact factor: 8.401

8.  Cellular RNA Targets of Cold Shock Proteins CspC and CspE and Their Importance for Serum Resistance in Septicemic Escherichia coli.

Authors:  Yael Yair; Charlotte Michaux; Dvora Biran; Jörg Bernhard; Jörg Vogel; Lars Barquist; Eliora Z Ron
Journal:  mSystems       Date:  2022-06-13       Impact factor: 7.324

9.  Pipasic: similarity and expression correction for strain-level identification and quantification in metaproteomics.

Authors:  Anke Penzlin; Martin S Lindner; Joerg Doellinger; Piotr Wojtek Dabrowski; Andreas Nitsche; Bernhard Y Renard
Journal:  Bioinformatics       Date:  2014-06-15       Impact factor: 6.937

Review 10.  Soil and leaf litter metaproteomics-a brief guideline from sampling to understanding.

Authors:  Katharina M Keiblinger; Stephan Fuchs; Sophie Zechmeister-Boltenstern; Katharina Riedel
Journal:  FEMS Microbiol Ecol       Date:  2016-08-21       Impact factor: 4.194

  10 in total

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