Use Case 2 - GREEKC

Use Case 2 HOW TO FIND DNA-TF / COACTIVATOR-TF ASSOCIATIONS THAT REGULATE TG

Biological question

Which DNA binding Transcription Factors (dbTFs) interact with a particular coactivator and regulate the transcription of target genes (TGs)?

The transcriptional coactivator CITED2 (Cbp/p300-interacting transactivator 2) is involved in many biological processes, such as cell differentiation and development of several tissues, (e.g., cardiac, adrenal, and neural tissues) (PMID: 21764344). Regulation of gene transcription can be accomplished through the interaction of a DNA binding TF (dbTF) with coactivator proteins (coTF), with the dbTF interacting with these coactivators important for the correct functioning of the target genes.

SOLUTION

To find the dbTFs interacting with a coactivator and the associated target genes, the BioGateway Cytoscape Plugin is used to display the interactions with CITED2 at both levels. The plugin can be downloaded from the Cytoscape App Store, and can launch queries to the BioGateway RDF Graph Database or ‘triple store’. A user can build a query consisting of several specific selection criteria. The output of the query is a network of nodes and edges connecting them, representing biological entities and the relationships between them.

BioGateway is an initiative that enables a Semantic Systems Biology approach. It provides an entry point to access a data warehouse where biological data is gathered in the form of triples (using RDF).
THE BIOGATEWAY RESOURCE

QUERY AND RESULTS

The specific questions are described in a stepwise manner in the lines of the Query Builder and the BioGateway options allow a specific further query.

FIRST SEARCH

a. In the first line of the Query Builder, the human protein CITED2 (Uniprot Accession Q99967, Cbp/p300-interacting transactivator 2) is selected as an entity, and the relationship “IntAct: molecularly interacts with” is selected to retrieve the protein:protein interactions that CITED2 has with different entities in a defined set A. At this point, the search can be run, the interactions can be imported into a new network and the resulting TFs of interest can be selected to subsequently find their TGs (Figure 1).

Figure 1. BioGateway Query Builder and First search results

The query is defined in the BioGateway Query Builder to first search for the proteins (TFs) that interact with CITED2 (Step 1). After the query is ran (Step 2), the results are imported into a new network and the query results are visualized with the BioGateway style.

SECOND SEARCH

b. By selecting the TF node EP300, the TGs of it can be found by using the BioGateway options (right-click menu). In this case, to find TGs, the “tfact2gene: involved in the regulation of” interactions FROM the node are selected (Figure 2).

c. The results from the last search are shown in a new Biogateway window. These interactions can be imported into the previous network and the layout can be changed for better visualization of all the resulting TG (Figure 3).

Figure 2. Steps to find the Second search results

From the EP300 node (dbTF), a pop-up menu comes, and the Biogateway option is selected (Step 1). Next, to find the TGs regulated by this node, the relations FROM this node (Step 2) and the “tfac2gene” type of relationship (Step 3) are selected for the query.

Figure 3. Visualization of the Second search results

The interactions from the Second query are selected, imported into the network form the First search (dbTFs), and the layout of the network is changed for better visualization.

INTERACTION REFERENCES

d. Finally, by double-clicking an interaction of interest, a new node in between is created. This last node can be selected and the BioGateway options (right-click menu) can be opened to find the source of this specific TF-TG and the PubMed ID of the paper from which the interaction was obtained (Figure 4).

Figure 4. Steps to find annotations from selected interaction

By double-clicking an interaction between the dbTF and a TG, a new node is created, and, from this one, the BioGateway options can be opened (Step 1). Then, the PubMed annotations of this interaction can be opened in an Internet explorer (Step 2).

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