Overview

The ComPlEx (Comparative analysis of Plant co-EXpression networks) tool provides an interactive comparison of co-expression networks across the PlantGenIE species and can be used to identify the sequence ortholog with the most conserved gene regulation.

Basic Usage

Input: ComPlEx compares two co-expression networks from two different species. There are two ways to get started:

1. Input gene ids in the left text box (separated by comma, tab or space) and select the appropriate species (X) in the drop down menu below. Then select the species to compare to (Y) in the right drop-down menu and click “Align X with Y”. The tool will display the co-expression network of the input gene set to the left (species X) and the co-expression network of their orthologs to the right (species Y).

2. Input gene ids of species X in the left text box and of species Y in the right text box. Select the appropriate species in the two drop down menus and click “Compare X to Y”. The tool will now display the two co-expression networks of the two input gene sets.

Co-expression. The co-expression threshold indicates the co-expression value required for two genes to be linked in the networks and can be changed using the slider. The co-expression values are z-scores computed from the initial correlation values (mutual information). For details, see the paper.

Network comparison. Blue links in the networks indicate conserved co-expression, while grey links represent co-expression only present in one species. A link between gene A and B in species X is conserved if a link exists between any of the orthologs of A and any of the orthologs of B in species Y. By selecting (clicking) a conserved (blue) link in one species, the corresponding link(s) in the other species will be highlighted (red). Correspondingly, selecting one or more genes (click a node or mouse-drag to select several nodes) in species X will highlight (red) the ortholog(s) in species Y (and vice versa). Next to the ortholog, a p-value will be displayed. This p-value indicates the conservation of the co-expression neighbourhood of that ortholog (i.e. to what degree the ortholog-pair share more co-expressed genes than what would be expected by chance). The p-value is computed using the entire network at a co-expression threshold of 2, that is, the p-values will often indicate conservation even though there are no conserved links in the displayed network.

Note that there is a (by default hidden) conservation slider that allows the user to regulate at what co-expression threshold conserved network links (i.e. blue links) are displayed. By default, this conservation threshold is the same as the co-expression threshold. By using the conservation slider to lower the threshold independently of the co-expression threshold, the user can add additional conserved links to the existing network without adding the accompanying non-conserved links. This can be useful when the network is already large, but should be used with caution as it will give a somewhat false sense of the level of network conservation.

Identifying co-expressed genes. Right-clicking a node in the networks and selecting “Add co-expressed genes” will add all genes with a correlation above the selected co-expression threshold to the network, and then re-align the two networks. If there are too many neighbours to be display, a warning will be appear, and you will have to increase the co-expression threshold before trying again.

Annotation table. The genes in each network is listed with annotations in a table below each network. Genes selected in the table are highlighted in the network and vice versa. Search functions are also implemented. There are buttons for adding selected genes to the gene lists of the respective species, and these gene lists can be used across the other PlantGenIE resources.

Orthologs. Orthologs were predicted using OrthoMCL with default parameters.

Data. ComPlEX uses in-house expression and annotation data generated by the UPSC Bioinformatics team.

Implementation. ComPlEX is implemented using JavaScript, PHP, MySQL, Cytoscape, Datatables and Toastr.