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. 2022 Dec 23;42(9):638–650. doi: 10.1038/s41388-022-02578-2

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© The Author(s) 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 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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Fig. 2 — A Localization of ribosomal proteins on the human 80S ribosome with significantly changed alternative splicing events of their encoding mRNAs in squamous cell carcinomas. Note that RPLP0 and RPLP2 were not included in the structure. B STRING interaction network analysis for the alternatively spliced genes in the GO term gene expression (GO:0010467) in squamous cell carcinomas compared to wild-type keratinocytes. C The translational efficiency of genes with differential alternative splicing events in the 5′UTR is increased in squamous cell carcinomas (SCC^c). Fold change in translation efficiency (TE) was computed for all genes or genes with significant alternative splicing events in the 5′UTR, coding sequence (CDS) or 3′UTR. Translation efficiency (ribosome profiling reads divided by RNA-seq reads) was computed using the LRT-test of the DESeq2 package. P-values indicate a two-sample Kolmogorov–Smirnov test comparing the TE distribution of genes with alternative splicing events to all genes. D Numbers and splicing categories of significantly changed alternative splicing events in squamous cell carcinomas (SCC^c) that alter either the 5′UTR, the coding sequence (CDS) or the 3′UTR. SS splice sites. E Most genes with differential 5′UTR isoforms in squamous cell carcinomas (SCC^c) express a set of transcripts that contain or exclude TOP motifs. StringTie transcripts of the 5′UTR isoforms and their 5′UTR sequences were assessed for the presence of TOP motifs as defined by a C at the +1 position and an unbroken series of 4–16 pyrimidines. Left panel shows the different 5′UTR isoform genes, while the colors indicate the fraction of StringTie transcripts that contain a 5′TOP motif between 0 and 1 (0 and 100%). Right panel, number of isoforms within the cohort of genes with 5′UTR isoforms in SCC^c that either contains a 5′TOP or do not contain a TOP motif. The color refers to the genes within the cohort of 5′UTR isoforms defined on the right side.