Banca de DEFESA: IGOR AUGUSTO BRANDÃO

Uma banca de DEFESA de MESTRADO foi cadastrada pelo programa.
STUDENT : IGOR AUGUSTO BRANDÃO
DATE: 24/08/2020
TIME: 14:30
LOCAL: Google Meet
TITLE:

Systems biology approaches in the investigation of articulation points in KEGG metabolic pathways

KEY WORDS:

Systems biology, KEGG, articulation point, metabolic pathway, network topology, network visualization.

PAGES: 61
BIG AREA: Ciências Biológicas
AREA: Biologia Geral
SUMMARY:

The study of proteins essentiality through laboratory methods is expensive, time-consuming and not scalable for large amounts of proteins. Besides, it is relevant to evaluate the essentiality of several proteins of a metabolic pathway as a whole. The metabolic pathways can be analyzed as graphs, which provide several tools to study the topological features such as the articulation points. Nowadays, research in bioinformatics studies the essentiality of proteins based on betweenness and degree metrics, however, graph theory suggests that articulation points could be essential nodes in a network. It remains to be determined whether these articulation points are essential in metabolic pathways and their topological impact on the network. Using network analysis via metrics and biologic curation, we aim to verify if bottlenecks are proteins with the highest frequencies and located in the center of KEGG metabolic pathways. For this purpose, we identified the articulation points in different networks, evaluate the impact of each articulation point, calculate their frequency and compare them with occurrences of non-articulation points. We consulted KEGG pathways available as KGML files. After, the data was transformed into a graph object. Two centrality parameters including articulation points and degree are determined and the essential proteins based on these parameters are classified. Approximately 20% of the proteins are articulation points. The articulation points with high- frequency which are located in central regions of the network were considered the most important (3.75%). In addition, the highest concentration of articulation points occurred in the frequency range of 80-90%. A pattern of non-randomness of articulation points was identified in the protein groups that have a frequency of at least 74.5%. Finally, steroid biosynthesis is the metabolic pathway with the highest number of articulation points with frequency higher than 80%. Besides, oxidoreductase is the articulation point class present in the highest number of metabolic pathways. Overall, the findings suggest that bottlenecks are articulation points with highest frequencies and located in the center of the network. It remains to perform a deep analysis on the articulation points biological roles.

BANKING MEMBERS:
Interno - 2276280 - CESAR RENNO COSTA
Externo à Instituição - RICARDO D'OLIVEIRA ALBANUS
Presidente - 1507794 - RODRIGO JULIANI SIQUEIRA DALMOLIN