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.

To overcome these limitations, a web-based interactive tool, so called LinkinPath, was developed to analyze, map, and visualize the gene/protein lists in the context of interconnected pathways, which provides a valuable resource for not only comprehensive studies of gene-gene interaction, but also functional genomics in virtually all organisms.

LinkinPath enables users to determine the cooccurrence and co-absence of genes or proteins on animated KEGG pathway maps as well as to compare functional compositions within and among the datasets using TreeMaps. Also, it will facilitate analyzing the statistically enriched pathways across the datasets and building the pathway-to-pathway networks for each dataset. Through LinkinPath, potential interaction/reaction paths between pathways can be explored, and common pathway-to-pathway networks across the datasets can also be identified.

Further information can be found in “LinkinPath: From Sequence to Interconnected Pathway”, published in Bioinformatics. LinkinPath was developed by BIOTEC Information Systems Laboratory and is freely available to all interested users at



Posted on 25 July 2011.