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Current Bioinformatics

Author(s): Ali Ghulam, Xiujuan Lei*, Min Guo and Chen Bian

DOI: 10.2174/1574893615999200413123352

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Comprehensive Analysis of Features and Annotations of Pathway Databases

Page: [803 - 820] Pages: 18

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Abstract

This study focused on describing the necessary information related to pathway mechanisms, characteristics, and databases feature annotations. Various difficulties related to data storage and retrieval in biological pathway databases are discussed. These focus on different techniques for retrieving annotations, features, and methods of digital pathway databases for biological pathway analysis. Furthermore, many pathway databases annotations, features, and search databases were also examined (which are reasonable for the integration into microarray examination). The investigation was performed on the databases, which contain human pathways to understand the hidden components of cells applied in this process. Three different domain-specific pathways were selected for this study and the information of pathway databases was extracted from the existing literature. The research compared different pathways and performed molecular level relations. Moreover, the associations between pathway networks were also evaluated. The study involved datasets for gene pathway matrices and pathway scoring techniques. Additionally, different pathways techniques, such as metabolomics and biochemical pathways, translation, control, and signaling pathways and signal transduction, were also considered. We also analyzed the list of gene sets and constructed a gene pathway network. This article will serve as a useful manual for storing a repository of specific biological data and disease pathways.

Keywords: Biological pathways, pathway databases, database features, pathway database annotations, metabolomics, gene.

Graphical Abstract

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