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. 2020 Oct 19;10:17597. doi: 10.1038/s41598-020-74483-1

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© The Author(s) 2020

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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Comparison of transcriptional profiles of FFPE—FF/OCT replicates. (A) A volcano plot of results for the linear model fit using weighted least squares for each gene performed on FFPE vs. FF/OCT expression is shown wherein the dashed line indicates an adjusted p-value = 0.05. Green points are genes that are differential for at least a log2 fold change of 2 and are significant after p-value adjustment. Genes for targeted clinical genomic tests (NCI tumor markers list) are shown in red. Several genes have been labeled to provide more insight into which genes are being represented. These labeled genes include those coding for the α subunit of glycoprotein hormones (CGA), beta-2-microglobulin (B2M), chorionic gonadotropin beta-subunit 2 (CGB2), fibrogen B beta chain (FGB), estrogen receptor 1 (ESR1), and kallikrein related peptidase 3 (KLK3). This scatter plot shows that none of these clinically important genes are differential between FFPE and FF/OCT replicates at statistically significant levels. (B) GSEA-based pathway enrichments of the differential expression analysis of FFPE vs. FF/OCT cohorts. All pathways listed here are up in FF samples. No statistically significant pathways were found up-regulated in FFPE samples.