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. 2023 Nov 25;24:713. doi: 10.1186/s12864-023-09816-1

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© The Author(s) 2023

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. 1 — Pathway Analysis with PFOCR. A Typical bar graph of Enrichr results for PFOCR pathways, above. Appyter UMAP of PFOCR pathway clusters, below. The Enrichment Analysis Visualizer appyter computed term frequency-inverse document frequency (TF-IDF) values for the gene set corresponding to each pathway in PFOCR and plotted the first two dimensions of a UMAP applied to the resulting values. Generally, pathways with more similar gene sets are positioned closer together. Pathways are colored by Leiden algorithm-computed clusters. B NDEx iQuery screenshot showing ranked pathway figures (left panel), original pathway figure of selected result (middle), and article metadata (right). The top-right includes buttons to a dedicated NDEx page or to import the figure-extracted gene set into Cytoscape as nodes. C The plot options for ORA and GSEA results in the R Shiny tool called Interactive Enrichment Analysis. PFOCR results include a view of the original published figure and a link to a dedicated PFOCR website page (right)