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. 2022 Feb 23;12:3080. doi: 10.1038/s41598-022-07151-1

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© This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply 2022

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/.

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Results of integrative ‘omics analysis of proteomic and transcriptomic data generated from IMR-90 cells with and without TGFβ1 treatment. (A) Transcriptomic module association with TGFβ1 treatment: Values in each cell represent correlation, in parentheses, with p-values between each module of co-expressed transcripts and TGFβ1 treatment. Heatmap shading corresponds to strength of association where darker red cells have higher upregulation and darker blue cells have higher downregulation based on correlation. Cells outlined in yellow withstand Bonferroni correction for multiple testing based on the number of modules generated. (B) Network visualization of hub genes in the blue transcriptomic module. Genes with a kME larger than 0.99 were selected for visualization in the blue module. The thickness of the edge corresponds to increasing topological overlap (TOM), a measure of the strength of correlation between transcript levels, which is the Pearson’s correlation obtained from the adjacency matrix. Nodes labeled in yellow correspond to single genes in the blue module that are annotated as associated with pirfenidone and/or nintedanib treatment. (C) Results from integration of transcriptomic and proteomic data. Values in each cell represent correlation, p-values in parentheses, between each module of co-expressed transcripts with TGFβ1 treatment and modules of co-expressed proteins. The y-axis corresponds to transcriptomic modules generated using WGCNA. The x-axis corresponds to the yellow and turquoise proteomic modules. Individually, the yellow and turquoise proteomic modules were significantly correlated with TGFβ1 treatment (depicted in Fig. 2).