Publication detail

Bipartite Graphs for Visualization Analysis of Microbiome Data

SEDLÁŘ, K. VÍDEŇSKÁ, P. ŠKUTKOVÁ, H. RYCHLÍK, I. PROVAZNÍK, I.

Original Title

Bipartite Graphs for Visualization Analysis of Microbiome Data

English Title

Bipartite Graphs for Visualization Analysis of Microbiome Data

Type

journal article in Web of Science

Language

en

Original Abstract

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.

English abstract

Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.

Keywords

metagenomics; OTU table; 16S rRNA; bipartite graph; visualization analysis; graph modularity

Released

31.05.2016

Publisher

Libertas Academica

Pages from

17

Pages to

23

Pages count

7

URL

Full text in the Digital Library

BibTex


@article{BUT125530,
  author="Karel {Sedlář} and Petra {Vídeňská} and Helena {Škutková} and Ivan {Rychlík} and Ivo {Provazník}",
  title="Bipartite Graphs for Visualization Analysis of Microbiome Data",
  annote="Visualization analysis plays an important role in metagenomics research. Proper and clear visualization can help researchers get their first insights into data and by selecting different features, also revealing and highlighting hidden relationships and drawing conclusions. To prevent the resulting presentations from becoming chaotic, visualization techniques have to properly tackle the high dimensionality of microbiome data. Although a number of different methods based on dimensionality reduction, correlations, Venn diagrams, and network representations have already been published, there is still room for further improvement, especially in the techniques that allow visual comparison of several environments or developmental stages in one environment. In this article, we represent microbiome data by bipartite graphs, where one partition stands for taxa and the other stands for samples. We demonstrated that community detection is independent of taxonomical level. Moreover, focusing on higher taxonomical levels and the appropriate merging of samples greatly helps improving graph organization and makes our presentations clearer than other graph and network visualizations. Capturing labels in the vertices also brings the possibility of clearly comparing two or more microbial communities by showing their common and unique parts.",
  address="Libertas Academica",
  chapter="125530",
  doi="10.4137/EBO.S38546",
  howpublished="online",
  institution="Libertas Academica",
  number="S1",
  volume="12",
  year="2016",
  month="may",
  pages="17--23",
  publisher="Libertas Academica",
  type="journal article in Web of Science"
}