A MapReduce tool for in-depth analysis of KEGG pathways: identification and visualization of therapeutic target candidates

• Published in: 2019 IEEE International Conference on Bioinformatics and Biomedicine (BIBM) pp. 2157 - 2162
• Main Authors: Palumbo, Giuseppe Alessandro Parasiliti, Biondi, Pietro, Sgroi, Giuseppe, Pennisi, Marzio, Russo, Giulia, Pappalardo, Francesco
• Format: Conference Proceeding
• Language: English
• Published: IEEE 01.11.2019
• Subjects: Biochemical Pathway; Genes; MAP3K8; MAPK1; MapReduce; Python; Therapeutic target
• DOI: 10.1109/BIBM47256.2019.8982978

Intracellular biochemical reactions emerge from the interaction among multiple extracellular signaling components. Considering the number, type and connections of the signaling components represents a needed step to characterize, identify and describe potential targets for a clinical purpose. However, it is increasingly documented that the presence of sub-types of signaling proteins, branching and crosstalk may lead to very variable outcomes in the same path, which is not always well defined experimentally. For this reason, we present an improved version of the algorithm based on the MapReduce paradigm to facilitate the discovery of new therapeutic targets. Our algorithm allows you to scan and perform a search in depth of biological pathway in order to analyze less recurrent and therefore non-trivial paths. These routes represent a chain of biochemical interactions among different biological actors that can be represented by quite distant nodes along the pathway. This type of analysis can also be performed manually, but with high execution times due to the large amount of pathways and genes present. Thus, our tool performs exhaustive analysis in an automated way, drastically reducing the time required. Our proposal allows us to discover the genes far from the initial target genes, also showing the number of occurrences of a given path found within the set of biological pathways analyzed during the simulation.