CyTargetLinker app update: A flexible solution for network extension in Cytoscape

LinkSets

On the CyTargetLinker website, we provide a variety of linksets for regulatory interactions, pathway associations and disease annotations (https://cytargetlinker.github.io/pages/linksets). Additionally, we deliver a simple Java program to convert tab delimited text files into XGMML linksets that can be used with CyTargetLinker (https://github.com/CyTargetLinker/linksetCreator). Using BridgeDb⁶, a framework for finding and mapping database identifiers, the script enables the support of multiple identifier systems for biological entities.

Application programming interface

While CyTargetLinker can still be used through the Cytoscape graphical user interface (see online tutorials), we would like to highlight the novel application programming interface (API) that allows the programmatic execution of the app’s functionality.

CyTargetLinker provides a set of API methods to automise the extension of networks (Table 1). The key function is the “extend” function, which parses the provided linksets and extracts relevant interactions for the selected network. The user can then choose to use the CyTargetLinker visual style and the force-directed layout. Often, users want to integrate knowledge for the same interaction type from different resources. With the “filterOverlap” function, users can visualise only those interactions that are supported by multiple resources.

Use cases highlighting the new automation functionality

Use case 1: Investigating drug-targets and disease associations for a Rett syndrome protein-protein interaction network. Rett syndrome is a rare disease caused by a mutation in the methyl-CpG-binding protein 2 (MECP2) gene⁷. In this use case, we used the stringApp⁸ of Cytoscape to create a protein-protein interaction (PPI) network for Rett syndrome (Disease Query). The PPI network is then extended using CyTargetLinker with compound-target interactions from ChEMBL^9,10 and disease-gene associations from a manually curated subset for rare diseases from OMIM¹¹. ChEMBL is an open online bioactivity database containing information about compounds, their bioactivity and their possible targets (including proteins). OMIM is a comprehensive collection of human genetic phenotypes and their associated human genes. First, the stringApp was used to create a Rett syndrome PPI (query=“Rett syndrome”, cutoff=0.4, limit=20). Using CyTargetLinker, the network was extended with 37 compound-target interactions from ChEMBL and 18 gene-disease associations from OMIM (see Figure 1).

The following API command was used to extend the network with compound-target and disease-gene information:

cytargetlinker extend
     idAttribute=”display name”
     linkSetFiles=”../LinkSets/chembl_23_hsa_20180126.xgmml,
           ../LinkSets/omim-rare-disease-has-20180411.xgmml”
     network=current

Figure 1. Compound-gene-disease network for Rett Syndrome.

The protein-protein interaction network for Rett syndrome was created using the disease query option of the stringApp for Cytoscape. The proteins are represented as gray circles. Then, CyTargetLinker was used to extend the network with compounds from ChEMBL (purple diamonds) and disease annotations from OMIM (blue octagons).

Use case 2: Pathway associations for differentially expressed genes in Rett syndrome. For this use case, we selected a list of differentially expressed genes in the Purkinje cells located in the cerebellar cortex of the brain of a Mecp2^−/y mouse model^12,13 for Rett syndrome. Next, we investigated in which biological processes these altered genes are involved. Using the pathway annotations from the WikiPathways database¹⁴, CyTargetLinker adds the pathway information and creates a pathway-gene network.

From the dataset, we extracted 65 genes with an absolute log2 fold change larger than 1. Only 16 genes are present in one or more pathways of the curated mouse pathway collection from WikiPathways. Figure 2 shows the resulting gene-pathway network. Genes without pathway annotations have been removed. Differential gene expression is shown on the gene nodes (blue = down, red = up) and green border color of the pathway nodes indicates that the pathway has been identified as significantly affected through overrepresentation analysis in the pathway analysis tool PathVisio¹⁵.

The following API command was used to extend the network with pathway information:

cytargetlinker extend
     idAttribute=”shared name”
     linkSetFiles=”../LinkSets/wikipathways-mm-20180410.xgmml”
     network=current
     direction=SOURCES

Figure 2. Gene-Pathway network for differentially expressed genes (DEGs) in Purkinje cells of Mecp2^−/y vs. wild type.

DEGs in a mouse model for Rett syndrome (Mecp2^−/y mice) were selected and imported in Cytoscape (circular nodes). The genes are colored based on changes in gene expression (blue=down-regulated, red=up-regulated). Thereafter, gene-pathway associations from WikiPathways were added and the pathways are shown as gray rectangles. Genes without pathway annotations have been removed. The green border color indicates pathways that are significantly altered based on over-representation analysis in PathVisio (Z-Score > 1.96).

Use case 3: Author-publication-journal network. This example uses two custom made linksets for author-article and article-journal relationships from Wikidata^16–18. After loading the initial five author nodes in Cytoscape, we performed a two-step extension with CyTargetLinker. We first added publications from the author-article linkset and then the journals from the article-journal linkset, see Figure 3. Author nodes are colored in gray, articles in yellow and journals in green. The network clearly shows the collaborations and diversity between the authors. Layout and visual style was slightly adapted manually in the graphical user interface to improve the readability of the network.

The following API commands were used to extend the network first with publication and then with journal information:

cytargetlinker extend
     idAttribute=”shared name”
     linkSetFiles=”../LinkSets/publications.xgmml”
     network=current

cytargetlinker extend
     idAttribute=”shared name”
     linkSetFiles=”../LinkSets/journals.xgmml”
     network=current

Figure 3. Author-Article-Journal network.

For the five authors of this manuscript, two custom linksets were used to first add author-article relationships and in a second step add article-journal relationships.