Constructing the microbial association network from large-scale time series data using granger causality

Dongmei Ai, Xiaoxin Li, Gang Liu, Xiaoyi Liang, Li C. Xia

Research output: Contribution to journalArticlepeer-review

1 Scopus citations

Abstract

The increasing availability of large-scale time series data allows the inference of microbial community dynamics by association network analysis. However, correlation-based association network analyses are noninformative of causal, mediating and time-dependent relationships between microbial community functional factors. To address this insufficiency, we introduced the Granger causality model to the analysis of a recent marine microbial time series dataset. We systematically constructed a directed acyclic network, representing both internal and external causal relationships among the microbial and environmental factors. We further optimized the network by removing false causal associations using the conditional Granger causality. The final network was visualized as a Granger graph, which was analyzed to identify causal relationships driven by key functional operators in the environment, such as Gammaproteobacteria, which was Granger caused by total organic nitrogen and primary production (p < 0.05 and Q < 0.05).

Original languageEnglish (US)
Article number216
JournalGenes
Volume10
Issue number3
DOIs
StatePublished - Mar 2019

Keywords

  • Conditional Granger causality
  • Granger causality
  • Marine microbes
  • Microbial association network
  • Time series data

ASJC Scopus subject areas

  • Genetics
  • Genetics(clinical)

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