Differential network analysis by simultaneously considering changes in gene interactions and gene expression

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review

3 Scopus Citations
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Author(s)

  • Jia-Juan Tu
  • Le Ou-Yang
  • Yuan Zhu
  • Hong Qin
  • Xiao-Fei Zhang

Related Research Unit(s)

Detail(s)

Original languageEnglish
Pages (from-to)4414-4423
Journal / PublicationBioinformatics
Volume37
Issue number23
Online published10 Jul 2021
Publication statusPublished - 1 Dec 2021

Abstract

Motivation: Differential network analysis is an important tool to investigate the rewiring of gene interactions under different conditions. Several computational methods have been developed to estimate differential networks from gene expression data, but most of them do not consider that gene network rewiring may be driven by the differential expression of individual genes. New differential network analysis methods that simultaneously take account of the changes in gene interactions and changes in expression levels are needed. Results: In this article, we propose a differential network analysis method that considers the differential expression of individual genes when identifying differential edges. First, two hypothesis test statistics are used to quantify changes in partial correlations between gene pairs and changes in expression levels for individual genes. Then, an optimization framework is proposed to combine the two test statistics so that the resulting differential network has a hierarchical property, where a differential edge can be considered only if at least one of the two involved genes is differentially expressed. Simulation results indicate that our method outperforms current state-of-the-art methods. We apply our method to identify the differential networks between the luminal A and basal-like subtypes of breast cancer and those between acute myeloid leukemia and normal samples. Hub nodes in the differential networks estimated by our method, including both differentially and nondifferentially expressed genes, have important biological functions.

Research Area(s)

  • BREAST-CANCER, THERAPEUTIC TARGET, LEUKEMIA, LASSO, SELECTION, PACKAGE, MODEL

Citation Format(s)

Differential network analysis by simultaneously considering changes in gene interactions and gene expression. / Tu, Jia-Juan; Le Ou-Yang; Yuan Zhu, ; Yan, Hong; Hong Qin; Zhang, Xiao-Fei.

In: Bioinformatics, Vol. 37, No. 23, 01.12.2021, p. 4414-4423.

Research output: Journal Publications and Reviews (RGC: 21, 22, 62)21_Publication in refereed journalpeer-review