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. 2024 Feb 8;16(3):641–663. doi: 10.1038/s44321-024-00028-y

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© The Author(s) 2024

Open Access This 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/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) CD64⁺MHCII⁺ and CD64⁺MHCII^- macrophages were sorted from CHIKV-infected joints (n = 5 animals per group) at 6 dpi and processed for RNA-seq. A total of 89 DEGs were identified. (B) Representative gene ontology terms and pathways are depicted, including genes involved in Th1 and Th2 differentiation as well as antigen processing and presentation. Analysis was carried out with a two-sided hypergeometric test, corrected with Bonferroni stepdown. ***P = < 0.001 (refer to Dataset EV1 for exact P values). (C) Gene ontology terms are presented as nodes and clustered together based on the similarity of genes present in each term or pathway. Ccr7, Cd74, Il12b, TBX21, and Serpinb9 are identified as genes highly associated with many of these terms. (D) A functionally grouped network of enriched pathways or terms based on the 89 DEGs were generated by querying the Gene Ontology - biological database with ClueGo. Source data are available online for this figure.