Improve Research Reproducibility A Bio-protocol resource
Concise Method
tooltip

Enrichment analysis for MICAL-L2 function

YY Yixing Yang
FY Fengwen Ye
TX Tianxiang Xia
QW Qianwen Wang
YZ Yujie Zhang
JD Jun Du
request Request a Protocol
ask Ask a question
Favorite

An ordered list of genes was generated based on the correlation between all genes and MICAL-L2 expression. Enriched pathways were determined using Gene Ontology (GO) [21, 22], KEGG [23–25], and GSEA [26, 27]. In the KEGG analysis, genes were determined to be differentially expressed based on a log2 fold-change of > 1.0 and an adjusted P-value < 0.05 (www.kegg.jp/kegg/kegg1.html), as previously reported [28]. “GSEA is a computational method that determines whether an a priori defined set of genes shows statistically significant, concordant differences between two biological states” [26, 27]. In this study, the predefined gene set was obtained from the MSigDB database (https://www.gsea-msigdb.org/gsea/msigdb/index.jsp). STRING (https://cn.string-db.org/) and Cytoscape were used to predict and display the protein-protein interaction network of MICAL-L2 co-expressed genes.

Copyright and License information: The Author(s) ©2022
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