Biological Network Mining

Zongliang Yue; Da Yan; Guimu Guo; Jake Y Chen

doi:10.1007/978-1-0716-1534-8_8

Biological Network Mining

Methods Mol Biol. 2021:2328:139-151. doi: 10.1007/978-1-0716-1534-8_8.

Authors

Zongliang Yue¹, Da Yan², Guimu Guo¹, Jake Y Chen¹

Affiliations

¹ The University of Alabama at Birmingham, Birmingham, AL, USA.
² The University of Alabama at Birmingham, Birmingham, AL, USA. yanda@uab.edu.

PMID: 34251623
DOI: 10.1007/978-1-0716-1534-8_8

Abstract

In this book chapter, we introduce a pipeline to mine significant biomedical entities (or bioentities) in biological networks. Our focus is on prioritizing both bioentities themselves and the associations between bioentities in order to reveal their biological functions. We will introduce three tools BEERE, WIPER, and PAGER 2.0 that can be used together for network analysis and function interpretation: (1) BEERE is a network analysis tool for "Biomedical Entity Expansion, Ranking and Explorations," (2) WIPER is an entity-to-entity association ranking tool, and (3) PAGER 2.0 is a service for gene enrichment analysis.

Keywords: Gene; Microarray; Network mining; Protein; Protein–protein interaction (PPI).

MeSH terms

Algorithms
Data Mining / methods*
Gene Regulatory Networks / genetics*
Humans
Programming Languages
Protein Interaction Maps / genetics*