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Table 1 Top 20 significantly differentially expressed protein coding genes between pRT responsive and non-responsive tumor samples

From: Molecular signature of response to preoperative radiotherapy in locally advanced breast cancer

# Gene Symbol Gene Name FDR-adjusted q-value Fold Change Super-Pathways
1 ST3GAL4 ST3 beta-galactoside alpha-2,3-sialyltransferase 4 0.03715 ## 0.10 protein glycosylation
2 C6orf105 (ADTRP) chromosome 6 open reading frame 105 (Androgen-Dependent TFPI-Regulating Protein) 0.03715 ## 0.17 No Data Available
3 RAP1GAP2 RAP1 GTPase activating protein 2 0.03781 ## 0.18 Immune System
4 A1CF APOBEC1 complementation factor 0.03874 ## 0.17 mRNA Editing and Processing of Capped Intron-Containing Pre-mRNA
5 MAP3K4 mitogen-activated protein kinase kinase kinase 4 0.03874 ## 0.25 MAPK signaling pathway
6 CHD5 chromodomain helicase DNA binding protein 5 0.05133 # 0.15 ATP-dependent helicase activity
7 LAS1L LAS1-like (S. cerevisiae) 0.05209 # 0.19 biogenesis of the 60S ribosomal subunit.
8 DEFB128 defensin, beta 128 0.05781 # 0.29 Immune System
9 ENHO energy homeostasis associated 0.05781 # 0.23 metabolism
10 CECR9 cat eye syndrome chromosome region, candidate 9 (non-protein coding) 0.05781 # 0.20 unknown
11 IDO1 indoleamine 2,3-dioxygenase 1 0.05781 # 0.20 Tryptophan metabolism
12 LRRC55 leucine rich repeat containing 55 0.05788 # 0.14 ion channel
13 ROGDI rogdi homolog (Drosophila) 0.05788 # 0.26 unknown
14 KRT25 keratin 25 0.05796 # 0.22 cytoskeleton
15 LAMA4 laminin, alpha 4 0.05798 # 0.25 Focal Adhesion, ECM-receptor interaction
16 PLA2G2C phospholipase A2, group IIC 0.05798 # 0.15 alpha-Linolenic acid metabolism and Glycerophospholipid biosynthesis
17 CCDC114 coiled-coil domain containing 114 0.05798 # 0.25 cell motility
18 CNGB1 cyclic nucleotide gated channel beta 1 0.05798 # 0.27 cAMP binding and intracellular cAMP activated cation channel activity
19 PRSS53 protease, serine, 53 0.05798 # 0.30 serine-type endopeptidase activity
20 GSG1 germ cell associated 1 0.05798 # 0.22 RNA polymerase binding
  1. FDR – false discovery rate; Fold change is shown on a linear scale
  2. #q-value < 0.1; ##q-value < 0.05