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. 2020 Feb 17;10:2734. doi: 10.1038/s41598-020-59516-z

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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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Differential expression and pathway analysis among subtypes of three cancers reveals differences in identified genes and pathways among pipelines. Schematics illustrate (a) differential expression analysis (b) pathway over-representation analysis and (c) Gene Set Enrichment (GSEA) analysis for each cancer comparison. Tables show number of differentially expressed genes/significantly impacted pathways for each comparison across each pipeline. Bar plots show the numbers of differentially expressed genes and pathways found or not-found by all pipelines.