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Table 1 Bcl-3 gene targets identified under various experimental conditions. (a) Genes identified in Bcl-3 ChIP-seq datasets (Ref [47]) that correspond to; (a) genes up-regulated in terminal end bud/branching morphogenesis (Ref [46]); (b) genes differentially regulated in 3D collagen I cultures versus basement membrane (Ref [49]); (c) genes regulated after knockdown of Bcl-3 in breast cancer cells (Ref [53]). Genes in bold are up-regulated under the experimental conditions, and all others were down-regulated

From: Multiple roles for Bcl-3 in mammary gland branching, stromal collagen invasion, involution and tumor pathology

(a) Mammary branching morphogenesis-associated gene expression. Up-regulated genes identified by both microarray of micro-dissected terminal end buds and Bcl-3 ChIP-seq data sets (Ref [43])
 TWIST2 Twist family bHLH transcription factor 2
 SNAI1 Snail family zinc finger 1
 FZD1 Frizzled class receptor 1
 FZD2 Frizzled class receptor 2
(b) Collagen invasion-associated gene expression. Genes identified in both Bcl-3 ChIP-seq datasets and in microarray analysis of mammary organoids cultured in 3D ECM versus 3D collagen I (Ref [41])
 DLK1 Delta-like 1 homolog (Drosophila)
 FERMT1 Fermitin family member 1
 CYR61 Cysteine-rich, angiogenic inducer, 61
 PTGS2 Prostaglandin-endoperoxide synthase 2 (prostaglandin G/H synthase and cyclooxygenase)
(c) Cell migration-associated gene expression. Genes identified in both Bcl-3 ChIP-seq datasets and in microarray analysis of gene expression following Bcl-3 knockdown in MDA231 (Ref [46]) and MG1361 breast cancer cells (Ref [32])
 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta
 RHOB Ras homolog family member B
 ARPC1A Actin-related protein 2/3 complex, subunit 1A, 41 kDa
 ARPC1B Actin-related protein 2/3 complex, subunit 1B, 41 kDa
 TUBB6 Tubulin, beta 6 class V
 ARPC4 Actin-related protein 2/3 complex, subunit 4, 20 kDa
 WASL Wiskott–Aldrich syndrome-like
 SSH2 Slingshot protein phosphatase 2
 NME1 NME/NM23 nucleoside diphosphate kinase 1
 NME2 NME/NM23 nucleoside diphosphate kinase 2
 NME3 NME/NM23 nucleoside diphosphate kinase 3
 ARHGDIB Rho GDP dissociation inhibitor (GDI) beta
 CDC42 Cell division cycle 42
 MYH9 Myosin, heavy chain 9, non-muscle
 DIAPH1 Diaphanous-related formin 1
 ENAH Enabled homolog (Drosophila)
 SSH3 Slingshot protein phosphatase 3
 ARHGAP1 Rho GTPase activating protein 1
 PAK1 p21 protein (Cdc42/Rac)-activated kinase 1
 ARPC3 Actin-related protein 2/3 complex, subunit 3, 21 kDa
 MYLK-AS1 MYLK antisense RNA 1
 PFN2 Profilin 2