A genome-scale co-functional network of xanthomonas genes can accurately reconstruct regulatory circuits controlled by two-component signaling systems

Hanhae Kim, Anna Joe, Muyoung Lee, Sunmo Yang, Xiaozhi Ma, Pamela C. Ronald, Insuk Lee

Research output: Contribution to journalArticle

Abstract

Bacterial species in the genus Xanthomonas infect virtually all crop plants. Although many genes involved in Xanthomonas virulence have been identified through molecular and cellular studies, the elucidation of virulence-associated regulatory circuits is still far from complete. Functional gene networks have proven useful in generating hypotheses for genetic factors of biological processes in various species. Here, we present a genome-scale co-functional network of Xanthomonas oryze pv. oryzae (Xoo) genes, XooNet (www.inetbio.org/ xoonet/), constructed by integrating heterogeneous types of genomics data derived from Xoo and other bacterial species. XooNet contains 106,000 functional links, which cover approximately 83% of the coding genome. XooNet is highly predictive for diverse biological processes in Xoo and can accurately reconstruct cellular pathways regulated by two-component signaling transduction systems (TCS). XooNet will be a useful in silico research platform for genetic dissection of virulence pathways in Xoo.

Original languageEnglish
Pages (from-to)166-174
Number of pages9
JournalMolecules and cells
Volume42
Issue number2
DOIs
Publication statusPublished - 2019 Jan 1

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Xanthomonas
Gene Regulatory Networks
Virulence
Biological Phenomena
Genome
Genetic Research
Genomics
Computer Simulation
Genes
Dissection

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Cell Biology

Cite this

Kim, Hanhae ; Joe, Anna ; Lee, Muyoung ; Yang, Sunmo ; Ma, Xiaozhi ; Ronald, Pamela C. ; Lee, Insuk. / A genome-scale co-functional network of xanthomonas genes can accurately reconstruct regulatory circuits controlled by two-component signaling systems. In: Molecules and cells. 2019 ; Vol. 42, No. 2. pp. 166-174.
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A genome-scale co-functional network of xanthomonas genes can accurately reconstruct regulatory circuits controlled by two-component signaling systems. / Kim, Hanhae; Joe, Anna; Lee, Muyoung; Yang, Sunmo; Ma, Xiaozhi; Ronald, Pamela C.; Lee, Insuk.

In: Molecules and cells, Vol. 42, No. 2, 01.01.2019, p. 166-174.

Research output: Contribution to journalArticle

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