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Analysis of topology properties in different tissues of poplar based on gene co-expression networks

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Abstract

Gene expression analysis is crucial for uncovering components underlying important biological processes for a focal organism. Large-scale gene co-expression networks generally exhibit small-world, scale-free properties; and the degree distributions of these networks follow power-law forms. Topology properties are often informative for determining the key components of the biological systems and their genetic mechanisms. Some basic topology properties display dissimilarity in different tissues, which helps to elucidate the different genetic mechanisms underlying important biological processes among tissues from the top to bottom of trees. In this study, the topology properties of gene co-expression networks were compared in leaf, shoot, wood, and root tissues of poplar. The comparison results demonstrated that the differences of topology properties exist among tissues and the root tissue displays larger average degree and network density, indicating that genes in root tissue are more highly co-expressed than those in the other three tissues. The nodes with a large degree, also known as hub genes, were annotated by the NetAffx Analysis Center and the agriGO tool, with annotation results that these highly interconnected genes are involved in the key biological processes in each tissue. This study also revealed the topology properties’ differences between gene co-expression networks and random network, suggesting the existence of hierarchically organized module and small-world organizations in networks of poplar. The approach described in this research offers an effective strategy for identifying key genes involved in the important biological processes in poplar.

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Data archiving statement

The detailed information of 231CEL files and some annotation results in this study are provided in the Supplementary files of Tables S1–S5. Microarray data of 231 CEL files with the accession number of GPL4359 in leaf, shoot, wood, and root tissues are available for download at Gene Expression Omnibus (GEO) http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL4359

Funding

This work was supported by the National Key Research and Development Plan of China (2016YFD0600101), and the National Natural Science Foundation of China (31570662 and 31500533). The funders guided the design of the study and participated in the manuscript revision.

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  1. College of Mechanical and Electrical Engineering, Nanjing Forestry University, Nanjing, 210037, China

    Huanping Zhang

  2. The Southern Modern Forestry Collaborative Innovation Center, Nanjing Forestry University, Nanjing, 210037, China

    Tongming Yin

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Correspondence to Huanping Zhang.

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Communicated by F. P. Guerra

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Table S1

Data series of Populus gene chips based on GPL4359 (XLSX 18 kb)

Table S2

AffyID of top lists of large degree nodes in four tissues (XLSX 17 kb)

Table S3

Annotation of large degree nodes in leaf, wood and shoot tissues (XLSX 19 kb)

Table S4

Annotated number in query list in shoot tissue by aigriGO (XLSX 12 kb)

Table S5

Significant GO terms in shoot tissue annotated by aigriGO (XLSX 16 kb)

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Zhang, H., Yin, T. Analysis of topology properties in different tissues of poplar based on gene co-expression networks. Tree Genetics & Genomes 16, 6 (2020). https://doi.org/10.1007/s11295-019-1400-3

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