DaGO-Fun - Database for GO-based Functional Annotation Analysis

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About Functional Networks

Technological developments in large-scale biological experiments, coupled with bioinformatics tools, have opened the doors to computational approaches for the global analysis of whole genomes. This has provided the opportunity to look at genes within their context in the cell. The integration of vast amounts of data generated by these technologies enhanced our understanding about processes involved in organism's metabolism, survival and development. As protein is a "social animal", i.e., a protein does not achieve its function alone but cooperates with other proteins to perform that function, these processes are accomplished through protein-protein interaction networks, therefore these play a central role in most activities involving the structure and function of the cell.

1. Protein-Protein Interactions

Interactions or relationships between proteins are of various types, but a high level description of biological systems partitions them into two categories, namely physical and functional interactions. Physical interactions refer to physical contact between proteins, and functional interactions or relationships between proteins involve the mechanism through which a particular protein achieves its functions. While "functional interactions" between proteins suggest direct physical contact between them, it is actually a broader concept and does not necessarily involve direct physical interactions. Here, we only refer to functional interactions or relationships, including physical and genetic interactions, and those derived from knowledge about co-expression and shared evolutionary history or pathways.
Proteins interact directly or indirectly through one or more intermediates to carry out their functions in promoting the stability and robustness of the system. These interactions can be modeled as a network, called a protein-protein functional network or interactome. This is a network in which nodes or vertices are proteins and edges or links represent pair-wise interactions or functional relationships between proteins within an organism. This approach provides the advantage of data integration, combining information from multiple interacting data sources into one unified network, leading to higher confidence and increased coverage.

2. Different Organism's Functional Networks

Existing genomic sequences and functional data are used to generate weighted functional interaction networks for Mycobacterial organisms and the human host for functional analyses at the system level and protein function prediction. Currently, the tool includes the following species:

  • Mycobaterium tuberculosis (MTB)
  • Mycobacterium leprae (MLP)
  • Mycobacterium smegmatis (MSM)
  • Human (Homo Sapiens)
  • Human-MTB (Host-Pathogen)

This can be viewed using the PINV (Protein Interaction Network Visualizer) tool, which is a web-based access tool, user friendly interface and an open source, providing fully interactive networks. The PINV tool is publicly available and accessible to all researchers working in applications involving protein analyses at the functional level.