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. 2024 Feb 8;25(3):1022–1054. doi: 10.1038/s44319-024-00075-z

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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/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Experimental approach to identify LINC00313 transcriptional targets. (B) Number of differentially expressed genes in pcLINC00313 versus pcDNA3 HuCCT1 cells (shrunken log2FC > 1, adjusted p-value < 0.1). Volcano plot shows differentially expressed genes (green colour: upregulated genes, red colour: downregulated genes). (C) KEGG pathway analysis of up or downregulated genes upon LINC00313 over-expression. (D) Example of GSEA of differentially expressed genes in response to LINC00313 over-expression. Shown is the enrichment of a Hippo signalling signature in the gene expression of cells overexpressing LINC00313. (E) WNT5A, AXIN2 and SULF2 mRNA levels in HuCCT1 expressing LINC00313 (pcLINC) or empty vector (pcDNA3). (F) WNT5A, AXIN2 and SULF2 expression in HuCCT1 transfected with siLINC00313 and stimulated with TGFβ1 or BSA/HCl for 16 h. Data information: In panel (B) statistically significant differential expressed genes were identified using DEseq2. In panel (C) adjusted p-value was calculated using the Benjamini-Hockberg method for correction for multiple hypotheses testing. In panel (D) GSEA results are displayed as a normalized enrichment score (NES) and presented as an enrichment plot. The Kolmogorov-Smirnov test was used for statistical analysis of GSEA. In (E,F) data are presented as mean ± SD (n = 3 biological replicates). *P ≤ 0.05, **P ≤ 0.01, ***P ≤ 0.001 (Student’s t-test). Source data are available online for this figure.