Explore gene-expression datasets with the Omics Dashboard

The advent of omics technologies has fostered the generation of a flood of complex, high-resolution datasets, the analysis of which remains a major hurdle and requires conversion into actionable biological knowledge. To address this challenge, Peter Karp and his colleagues from the SRI Bioinformatics Research Group have developed the Omics Dashboard within the BioCyc.org website. Here, they present their tool and its main features.

The Omics Dashboard

The Dashboard provides a multi-level visual read out of an expression dataset, from the cellular level to the gene level.  The user can probe their data in a fast and intuitive manner to gain a deep understanding of the data at multiple biological levels.

 

At the highest echelon (Figure 1) the Dashboard provides a set of panels for cellular systems such as degradation, biosynthesis, and energy metabolism.  Each panel contains a set of plots that graph the aggregate behavior of subsystems within each system. For example, in Figure 1, which is derived from an Escherichia coli dataset in which the bacterium transitions from anaerobic to aerobic growth, we see increases in gene expression for most biosynthetic systems, although carbohydrate degradation decreases.

 

In each panel, the colored vertical bars represent the six time points in this dataset; each dot represents a single gene expression measurement, and the fat dots encode the averages of all the data for that time point.  If you allow your eye to follow the fat dots, you will see the aggregate behavior of each subsystem. Note that Figure 1 omits several panels at the bottom; for a complete list, click on the second row in the table of Omics Dashboard examples at https://biocyc.org/dashboard/dashboard-intro.shtml.

 

Gene expression measurement omictools

 

Within the Biosynthesis panel, clicking on the “AA Syn” plot produces Figure 2, which shows the expression levels of each individual amino acid biosynthetic pathway as a separate plot.  Again, vertical bars represent time points, small dots represent gene expression measurements for individual genes within the pathway, and fat dots represent averages.

 

Expression levels of each individual amino acid biosynthetic pathway OMICtools

 

Clicking on the plot for Met produces Figure 3, which provides a detailed plot of every gene within the pathway for methionine biosynthesis.

 

 detailed plot of every gene within the pathway for methionine biosynthesis

 

The Dashboard provides many options for customizing these displays, such as switching between log and linear plots, sorting the plots within a panel according to many options, and adding additional custom plots and panels to the Dashboard.  The software will also generate operon diagrams and pathway diagrams (Figure 4) painted with gene expression data.

 

Gene expression data are supplied in a tab-delimited file with gene names or identifiers in the first column and data values in subsequent columns.  Before importing a dataset, be sure to select the BioCyc organism to which your data applies using the selector in the upper right corner.

 

Gene expression OMICtools

Omics Dashboard availability

The Omics Dashboard is available as both, a web application and as part of the downloadable Pathway Tools software: the web version of the Omics Dashboard is freely available in conjunction with the EcoCyc E.coli database at BioCyc.org; a subscription is required for its use with other BioCyc databases.

 

In conjunction with the downloadable Pathway Tools (see https://biocyc.org/download.shtml for download instructions) the Omics Dashboard is freely available for academic research purposes for application to any organism; a fee applies to other types of use.

Reference

Paley et al. (2017). The Omics Dashboard for interactive exploration of gene-expression data. Nucleic Acids Research.