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. 2024 Jul 27;43:209. doi: 10.1186/s13046-024-03129-1

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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/. 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.

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Fig. 6 — RNA-Seq analysis of Eo-EV signatures. A RNA Transcript biotypes distribution into the two indicated EV signatures. Classification was performed according to the ENSEMBL official transcript definition (https://www.ensembl.org/info/genome/genebuild/biotypes.html). Values depict the percentages of the indicated biotypes, expressed as the mean read per each biotype versus the total number of reads. B Distribution of differentially expressed protein-coding mRNAs alongside the indicated Eo-EV signatures. Volcano plot shows the p values (Y axis, negative base 10 logarithm) distribution versus the mean Fold Change (X axis, base 2 logarithm). Colored dots represent significant (-log10(p value) > 1.3) mRNAs whose mean FC is upregulated (log2(Fold Change) > 1, Eo33-EV) or downregulated (log2(Fold Change) < 1, Eo5-EV). Grey lines represent the p value and Fold Change settings employed to select statistically significant upregulated/downregulated mRNAs (italic numbers). C Differential expression of the significant genes (as delineated in panel B) for the Eo-EV signatures compared to the two experimental conditions. Heatmap shows the base 2 logarithm of the 88 and 132 differentially expressed genes into the replicates (R1, R2) for each Eo-EV signature. Dendrograms show hierarchical clustering for experimental conditions (EXO5 for Eo5-EV, EXO33 for Eo33-EV) and mRNAs. Gene expression has been clustered by K-means method (n = 60). Tumor suppressor genes (provided by the CancerMine and TSGene databases) are indicated for each Eo-EV signature with their respective percentage (number of tumor suppressors versus total genes into the signature)