Network Modeling of Complex Data Sets

Methods Mol Biol. 2020:2096:197-215. doi: 10.1007/978-1-0716-0195-2_15.

Abstract

We demonstrate a selection of network and machine learning techniques useful in the analysis of complex datasets, including 2-way similarity networks, Markov clustering, enrichment statistical networks, FCROS differential analysis, and random forests. We demonstrate each of these techniques on the Populus trichocarpa gene expression atlas.

Keywords: Differential analysis; Enrichment; FCROS; Fisher exact test; Machine learning; Random forests; Similarity network.

Publication types

  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Algorithms
  • Cluster Analysis
  • Databases as Topic*
  • Gene Expression Regulation, Plant
  • Gene Regulatory Networks*
  • Populus / genetics*
  • Software