The mammalian protein-protein interaction database and its viewing system that is linked to the main FANTOM2 viewer

Abstract

Here, we describe the development of a mammalian protein-protein interaction (PPI) database and of a PPI Viewer application to display protein interaction networks (http://fantom21.gsc.riken.go.jp/PPI/). In the database, we stored the mammalian PPIs identified through our PPI assays (internal PPIs), as well as those we extracted and processed (external PPIs) from publicly available data sources, the DIP and BIND databases and MEDLINE abstracts by using FACTS, a new functional inference and curation system. We integrated the internal and external PPIs into the PPI database, which is linked to the main FANTOM2 viewer. In addition, we incorporated into the PPI Viewer information regarding the luciferase reporter activity of internal PPIs and the data confidence of external PPIs; these data enable visualization and evaluation of the reliability of each interaction. Using the described system, we successfully identified several interactions of biological significance. Therefore, the PPI Viewer is a useful tool for exploring FANTOM2 clone-related protein interactions and their potential effects on signaling and cellular communication.

Figure 1

RIKEN PPI database. (A) Overview of the database. The number of interactions obtained from each data source is shown near the arrows. The interactions from DIP and BIND public database are updated regularly, and the interactions from the internal experiments and FACTS are also updated in a timely fashion. (B) The table structure of the PPI database. Each box represents a table and contains the table name at the top, followed by the column names. The arrows and equation labels indicate corresponding column names between two tables. Using this correspondence, exactly one entry in the table at the end of the arrow can be identified by using a corresponding value in the column of the table at the beginning of the arrow. A specific entry in the FANTOM2 database can be retrieved by using the clone ID as a key. The various tables are:

1. ppi_primers: Contains primer IDs as well as primer sequences and clone IDs. A protein sequence can be estimated by using this table and the RIKEN cDNA database.

2. ppi_function: Includes the functional annotation for each RIKEN clone.

3. interaction: Comprises a list of interactions identified through our assays (internal PPIs).

4. ext_interaction: Stores a list of interactions extracted from publicly available data sources (external PPIs).

5. ext_protein: Includes protein information of the external PPIs. Each protein is identified by its NCBI accession number.

6. ppi_source: Stores information regarding the origin of the interactions, i.e., RIKEN_PPI assay, DIP, BIND, or literature.

7. homology: Contains the results of homology searches and the alignment of two sequences.

Figure 1

RIKEN PPI database. (A) Overview of the database. The number of interactions obtained from each data source is shown near the arrows. The interactions from DIP and BIND public database are updated regularly, and the interactions from the internal experiments and FACTS are also updated in a timely fashion. (B) The table structure of the PPI database. Each box represents a table and contains the table name at the top, followed by the column names. The arrows and equation labels indicate corresponding column names between two tables. Using this correspondence, exactly one entry in the table at the end of the arrow can be identified by using a corresponding value in the column of the table at the beginning of the arrow. A specific entry in the FANTOM2 database can be retrieved by using the clone ID as a key. The various tables are:

1. ppi_primers: Contains primer IDs as well as primer sequences and clone IDs. A protein sequence can be estimated by using this table and the RIKEN cDNA database.

2. ppi_function: Includes the functional annotation for each RIKEN clone.

3. interaction: Comprises a list of interactions identified through our assays (internal PPIs).

4. ext_interaction: Stores a list of interactions extracted from publicly available data sources (external PPIs).

5. ext_protein: Includes protein information of the external PPIs. Each protein is identified by its NCBI accession number.

6. ppi_source: Stores information regarding the origin of the interactions, i.e., RIKEN_PPI assay, DIP, BIND, or literature.

7. homology: Contains the results of homology searches and the alignment of two sequences.

Figure 2

Screen display of the PPI Viewer. The viewer consists of the Interaction List (A) and the Interaction Network (B). The Interaction List displays all the deposited PPIs sorted according to the proteins' IDs. For internal PPIs, the list can be sorted according to bait (BIND) or prey (ACT) proteins. The listed data include the interaction pairs and their annotations, supplemented with information of the primer sequences for construction of the assay samples and the luciferase activity (LUC) of the interaction (internal PPIs) or the data source linked to the MEDLINE abstracts (external PPIs). Clone IDs in the list are linked to the main FANTOM2 viewer (right lower inset). Some clone IDs are linked to the RIKEN 3′-end-sequence database with homology information because we have used several RIKEN clones that correspond to mouse known genes and therefore have not been fully sequenced. Accession IDs (GI number) in the external interaction list are linked to the NCBI clone viewer. These links enable users to obtain detailed information on the clone. The Interaction Network (B) comprises three sections labeled Search, Assay Type List, and Interaction Link. In the Search section, users can search for a clone to display according to any part of letters or numbers in its clone ID, accession ID, or GI number. Users also can search for proteins by KEYWORD. For example, entering “death” as a keyword yields clone 2010323J02 (programmed cell death 6). LUC, CONFIDENCE, and LEVEL are parameters with which users can display interactions having the desired luciferase activity, confidence and within the desired number of interaction steps from the target protein, respectively. In the Assay Type List section, interactions from selected data sources can be color-coded (red, green, or blue). In the Interaction Link section, the protein interaction network for the target protein (shown as a red node) is displayed as edges and nodes. The luciferase activity (LUC) and confidence of an interaction are reflected by the thickness of its edge. For internal PPIs, an arrow indicates the direction of bait protein to prey protein in the mammalian two-hybrid assay. Self-interactions are shown as double boxes, and integrated genes are shown as a single node with an asterisk. The interaction network is labeled with IDs (default) or with both IDs and annotations (by clicking the View and Hide buttons). The APPLET SIZE and length of edges (pulldowns to the right of the Hide button) can be changed. Brief instructions are listed in Table 1.

Figure 2

Screen display of the PPI Viewer. The viewer consists of the Interaction List (A) and the Interaction Network (B). The Interaction List displays all the deposited PPIs sorted according to the proteins' IDs. For internal PPIs, the list can be sorted according to bait (BIND) or prey (ACT) proteins. The listed data include the interaction pairs and their annotations, supplemented with information of the primer sequences for construction of the assay samples and the luciferase activity (LUC) of the interaction (internal PPIs) or the data source linked to the MEDLINE abstracts (external PPIs). Clone IDs in the list are linked to the main FANTOM2 viewer (right lower inset). Some clone IDs are linked to the RIKEN 3′-end-sequence database with homology information because we have used several RIKEN clones that correspond to mouse known genes and therefore have not been fully sequenced. Accession IDs (GI number) in the external interaction list are linked to the NCBI clone viewer. These links enable users to obtain detailed information on the clone. The Interaction Network (B) comprises three sections labeled Search, Assay Type List, and Interaction Link. In the Search section, users can search for a clone to display according to any part of letters or numbers in its clone ID, accession ID, or GI number. Users also can search for proteins by KEYWORD. For example, entering “death” as a keyword yields clone 2010323J02 (programmed cell death 6). LUC, CONFIDENCE, and LEVEL are parameters with which users can display interactions having the desired luciferase activity, confidence and within the desired number of interaction steps from the target protein, respectively. In the Assay Type List section, interactions from selected data sources can be color-coded (red, green, or blue). In the Interaction Link section, the protein interaction network for the target protein (shown as a red node) is displayed as edges and nodes. The luciferase activity (LUC) and confidence of an interaction are reflected by the thickness of its edge. For internal PPIs, an arrow indicates the direction of bait protein to prey protein in the mammalian two-hybrid assay. Self-interactions are shown as double boxes, and integrated genes are shown as a single node with an asterisk. The interaction network is labeled with IDs (default) or with both IDs and annotations (by clicking the View and Hide buttons). The APPLET SIZE and length of edges (pulldowns to the right of the Hide button) can be changed. Brief instructions are listed in Table 1.

Figure 3

Analysis of interaction networks with the PPI Viewer. (A) Protein interactions involved in the formation of COPII vesicles. The components of COPII vesicles, Sec23 and Sec31, are connected by two interactions derived from internal (red edge) and external (blue edge) PPIs. (B) Interaction of LIM domain proteins with single-stranded-DNA-binding protein 2 (SSBP2, clone ID 2310079I02). Our PPI assay identified 14 interaction partners of this clone; but setting the luciferase reporter activity parameter to 3 reduced the number of displayed proteins to only 4.

Figure 3

Analysis of interaction networks with the PPI Viewer. (A) Protein interactions involved in the formation of COPII vesicles. The components of COPII vesicles, Sec23 and Sec31, are connected by two interactions derived from internal (red edge) and external (blue edge) PPIs. (B) Interaction of LIM domain proteins with single-stranded-DNA-binding protein 2 (SSBP2, clone ID 2310079I02). Our PPI assay identified 14 interaction partners of this clone; but setting the luciferase reporter activity parameter to 3 reduced the number of displayed proteins to only 4.