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. 2023 Oct 13;14:6446. doi: 10.1038/s41467-023-41919-x

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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 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. 5 — a Top 25 GO terms enriched for genes proximal to gained active and open regions in GB (peaks <2 kb TSS) (p-value: hypergeometric test with Benjamini correction). b Expression of DEGs related to synapse and glutamatergic synapse (top), and axon guidance and axonogenesis (bottom) located <2 kb from a gained active/open peak. c Intersection of the 497 DEGs with the HOMER significantly enriched motifs at the gained regions or anchors of differential loops identifies 11 key TFs (p-values: hypergeometric test). d Expression of PITX1 and SMAD3 downstream target genes (i.e., motif enrichment at a differential peak <2 kb TSS) among the DEGs in GB vs normal astrocytes (common targets in bold). e Top GO terms enriched for SMAD3, PITX1 and SIX1 proximal downstream target genes (p-value: hypergeometric test with Benjamini correction). f Sample-to-sample distance for GB (glioblastoma, n = 156) or LGG (low-grade glioma, n = 511) tumours from TCGA based on the expression of the SMAD3 and PITX1 downstream targets. Annotations include 1p/19q co-deletion and non codel (i.e., 1p/19q intact), as well as LGG oligodendrogliomas.