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

(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