LinkinPath: a web-based interactive exploration tool for pathway analysis

Pathways are functional units resulted from the interplay of interacting genes, RNAs, proteins and small molecules. Mapping genes or proteins into the context of pathways can help gain more insights into their functions and interactions in an organism. Although sequence similarity based methods have been commonly used for identification of pathways to genes/proteins based on their orthologous genes/proteins annotated in the well-characterized pathways, these methods have limitations such that some best hits may not necessarily be annotated in any pathway. The incorporation of additional data such as protein-protein interactions and enzymatic reactions can help infer the pathways and their interconection and uncover the biological function of genes/proteins. However, the information regarding the connections between pathways through molecular interactions and reactions are not included and adequately represented to support the exploratory analysis in most pathway mapping tools [link].


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