APID: Agile Protein Interaction DataAnalyzer

Description

APID (Agile Protein Interaction DataAnalyzer) is an interactive bioinformatic web-tool that has been developed to allow exploration and analysis of main currently known information about protein-protein interactions integrated and unified in a common and comparative platform. The analytical and integrative effort done in APID provides an open access frame where all known experimentally validated protein-protein interactions (BIND, BioGRID, DIP, HPRD, IntAct and MINT) are unified in a unique web application that allows an agile exploration of the interactome network and includes certain calculated parameters that weight the reliability of a given interaction (i.e. the "edges" of the interactome network) between two proteins, and also qualify the functional environment around any given protein (i.e. the "nodes" of the interactome network) . Such parameters are:
... about the proteins:

... about the interactions:

APID can be explored in an interactive way via open web access, and also includes a graphic tool to visualize and browse upon the interactions network. This tool is called APIN (Agile Protein Interaction Navigator) (see De Las Rivas et al., 2004). The APIN tool reads data from a selected set of interactions and displays the proteins and interactions in an interactive customizable way, like a browser. In this way, using an intuitive and clear interface one can navigate into complex interactome networks focusing on some areas, or on some specific proteins, by applying restrictions to the queried data. Finally, a clear aim of APID tool is to provide interaction's quality cut offs based on the parameters described above, in order to facilitate the researchers to find out the biological information and knowledge that the currently known interactomes include about a given query protein or group of proteins.

Using APID the interactions for a given query protein can be exported from the web view using the Export button that provides a tabulated .txt file including information in six columns corresponding to: UniProt_Names of each interacting protein pair; number of experimental methods that prove such interaction; iPfam validation; provenance source databases that include such interaction; GO overlapping terms for such protein pair.

Technical development

APID has been set up after the analysis of several available databases of protein-protein interactions. At present time, it includes the information from six main source databases: BIND (Biomolecular Interaction Network Database), BioGRID (The General Repository for Interaction Datasets), DIP (Database of Interacting Proteins), HPRD (Human Protein Reference Database), IntAct (Database system and analysis tools for protein interaction data) and MINT (Molecular Interactions Database). As HUPO PSI indicates (see http://psidev.sourceforge.net/), in these databases the data are provided in many different formats and are not synchronized. Moreover, we have observed that the data included in such databases are quite heterogeneous and the protein-protein interaction information has little overlap. APID includes a web page on statistics that shows the overlapping and specificity of the source data as far as we have been able to integrate and evaluate them. APID uses the UniProt IDs as the main relational key for all the proteins, linking each time to UniProt database. In this way, we avoid to introduce any new arbitrary key or ID and this facilitates a more sensible approach that keeps the link to the standard Universal Protein database. For a correct identification of each protein and to avoid redundancy we have used a sequence-based approach running BLAST2 algorithm for each protein comming from different data sources. This is also important because many times the proteins names, protein symbols and protein IDs given by each data source are very confusing.

The integration of the original data in APID web server has been done including all the information about proteins, interactions, species, experimental methods, PubMed publications references, PSI-MI controlled vocabulary references (http://psidev.sourceforge.net/mi/xml/doc/user/), and links to to each source database and to other resource biomolecular databases: UniProt, NCBI Gene, Ensembl Gene, Pfam, InterPro and Gene Ontology (GO). All the work-flow for APID and APIN has been developed in Java and the web interface follows a J2EE architecture.

Figures about APID

As indicated above, the detailed figures about the information integrated in APID are presented in the enclosed web page entitle statistics that includes:

Definition and meaning of Protein-Protein Interaction

At present APID, to be clear and quick, includes only data on a first level of protein association that corresponds to the most restricted meaning of interaction: i.e. co-interacting proteins, defined as proteins that have physical interaction. Further development of the web-tool will explore other types of protein association: co-functional proteins, defined as proteins that are involved in the same biomolecular pathway; co-expressed proteins, defined as proteins whose transcripts are expressed at the same time during cellular function; co-located proteins, defined as proteins that work in the same cellular compartment.

Raw Data

More information about the raw data present in this web-tool and about the versions of the source databases that have been used to build APID can be found in Data. As indicated above, APID is a bioinformatic web server that integrates and unifies multiple source databases facilitating to query and explore together in an agile way main known interactomes information experimentally-validated. APID complete data can not be redistributed because they do not belong to an own database and because the source databases have different legal requirements and download policies. Most of these databases are open access and public for academics and research, to download we recommend to contact the original source databases at their webs quoted (see also Links).

Citing APID

- Prieto C. and De Las Rivas J. (2006). APID: Agile Protein Interaction DataAnalyzer. Nucl. Acids Res. 34: W298-W302. PMID: 16845013.

Some Other References

- Hernandez-Toro J., Prieto C. and De Las Rivas J. (2007). APID2NET: unified interactome graphic analyzer. Bioinformatics 23(18): 2495-2497. PMID: 17644818.
- De Las Rivas J. and De Luis A. (2004). Interactome data and databases: different types of protein interaction. Comparative and Functional Genomics. 5: 173-178.
- De Las Rivas J., Prieto C. and De Luis A. (2004). Exploring Protein Interaction Networks and Functional Relationships at a Genomic Scale with a Agile Browser. Proceedings of the 1st Structural Bioinformatics Meeting. 73, 80 - 81.

Contact

For any query or suggestion please contact:
- Carlos Prieto: cprietos@usal.es
- Javier De Las Rivas: jrivas@usal.es