Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Weighted gene co-expression network analysis (WGNCA)

HW Haijing Wang
DL Daoxin Liu
PS Pengfei Song
FJ Feng Jiang
XC Xiangwen Chi
TZ Tongzuo Zhang
request Request a Protocol
ask Ask a question
Favorite

To perform unsigned WGCNA analysis, we used the R WGCNA package (https://cran.r-project.org/package=WGCNA) [72]. (Soft-power 5, mergeCutheight 0.25, minModuleSize 30). We identified 5 modules. Module-Trait relationships were calculated by Pearson correlation between the eigengene of each module and the specific phenotype data. Module eigengenes and orthogroup connectivity were calculated separately in each network using the moduleEigengenes() and intramodularConnectivity() functions in WGCNA, respectively.

Protein–protein interaction (PPI) networks can assist in the identification of key genes and pivotal gene modules involved in the response to hypoxia. Relations between genes were visualized by means of Cytoscape (v3.8.0) [73]; MCODE verified the key modules, and the hub gene were identified with cytoHubba. To explore the relationship among three transcription factors (TFs), we used ChEA3 [74]. ChEA3 is a database that performs TFs enrichment analysis based on ChIP-seq experiments.

Copyright and License information: The Author(s) ©2021
Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Do you have any questions about this protocol?

Post your question to gather feedback from the community. We will also invite the authors of this article to respond.

post Post a Question
0 Q&A