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. 2019 Aug 2;47(18):e111. doi: 10.1093/nar/gkz655

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 5. — Experimental validation of LTMG-DGE. (A) Overlap of down-regulated genes in APE1/Ref-1-KD vs. SCR control in hypoxia and normoxia, identified by LTMG-DGE and MAST. (B) Enrichment of the genes down-regulated in APE1/Ref-1-KD versus SCR control in key APE1/Ref-1 related pathway, under hypoxic conditions. (C) Expression of selected genes analyzed by qPCR of Pa03C cells transfected with APE1/Ref-1 siRNA and placed under hypoxia for 24 h. (D–F) Expression profile of SLC2A3 and PARP4 in APE1/Ref-1-KD (siAPE) and control (SCR) under hypoxia. Gene expression level is quantified by log(RPKM) and represented on the x-axis. Gold and blue curves represent peaks correspond to different TRSs. (G) Bi-cluster structures of gene coregulation modules enriched by STAT3 and HIF1A regulated genes. The x-axis represents samples and y axis represents genes. AE and SE status of a gene in a sample are colored by red and blue, respectively.