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Table 2 Dominant gene signatures induced by transforming growth factor-β1 in the mesenchymal MDA-MB-231 CN and MDA-MB-231 H2 cell lines

From: HER-2 overexpression differentially alters transforming growth factor-β responses in luminal versus mesenchymal human breast cancer cells

Sequence namea Sequence descriptionb Fold Δ MB-231 CNc Fold Δ MB-231 H2d Gene ontologye
ANGPTL4 Angiopoietin-like 4   3.34 Angiogenesis
EDN1 Endothelin 1 (ET-1) 2.87 2.45 Angiogenesis
VEGF Vascular endothelial growth factor   2.16 (4) Angiogenesis
DAAM1 Dishevelled associated activator of morphogenesis 1   3.58 Cytoskeleton regulation
FSCN1 Fascin homolog 1, actin-bundling protein   2.71 Cytoskeleton regulation
KRT7 Keratin 7   1.71 Cytoskeleton regulation
KRTHB1 Keratin, hair, basic, 1   1.70 Cytoskeleton regulation
MYO10 Myosin X 2.13 2.16 Cytoskeleton regulation
NEDD9 Neural precursor cell, developmentally down-regulated 9   2.56 Cytoskeleton regulation
PLEK2 Pleckstrin 2 4.62 3.80 Cytoskeleton regulation
PODXL Podocalyxin-like 3.07 1.92 Cytoskeleton regulation
PDLIM4 LIM domain protein, Reversion-induced LIM protein (RIL)   1.95 Cytoskeleton regulation
SMTN Smoothelin   2.02 Cytoskeleton regulation
SPAG4 Sperm associated antigen 4   2.60 Cytoskeleton regulation
TAGLN Transgelin 2.21 3.35 Cytoskeleton regulation
TPM1 Tropomyosin 1 (alpha) 1.90 (3) 2.42 (3) Cytoskeleton regulation
TUBA3 Tubulin, alpha 3   2.04 Cytoskeleton regulation
COL1A1 Collagen, type I, alpha 1 10.10 18.47 (2) ECM/adhesion
COL4A1 Collagen, type IV, alpha 1 5.08 (2) 3.94 (2) ECM/adhesion
COL4A2 Collagen, type IV, alpha 2 3.10 (2) 2.40 (2) ECM/adhesion
COL5A1 Collagen, type V, alpha 1   3.71 (3) ECM/adhesion
COL6A3 Collagen, type VI, alpha 3   20.61 ECM/adhesion
COL7A1 Collagen, type VII, alpha 1   3.74 (2) ECM/adhesion
FN1 Fibronectin 1   2.22 (4) ECM/adhesion
ITGA2 Integrin, alpha 2 (CD49B, alpha 2, VLA-2 receptor)   1.85 ECM/adhesion
ITGA5 Integrin, alpha 5 (fibronectin receptor)   2.58 ECM/adhesion
ITGB1 Integrin, beta 1 (fibronectin, receptor, beta)   3.13 ECM/adhesion
LAMC2 Laminin, gamma 2   7.84 (2) ECM/adhesion
MFAP2 Microfibrillar-associated protein 2   2.15 ECM/adhesion
SDC1 Syndecan 1   2.25 (2) ECM/adhesion
THBS1 Thrombospondin 1 5.15 (4) 3.03 (4) ECM/adhesion
CLDN4 Claudin 4   1.78 ECM/adhesion
ADAM19 A disintegrin and metalloproteinase domain 19 2.42 3.12 Protease and inhibitors
FURIN Furin (paired basic amino acid cleaving enzyme) 2.57 2.56 Protease and inhibitors
MMP14 Matrix metalloproteinase 14 (membrane-inserted) 2.19 1.85 (2) Protease and inhibitors
PRSS3 Protease, serine, 3 (mesotrypsin)   3.19 (2) Protease and inhibitors
PLAU Plasminogen activator, urokinase 2.02 (2) 2.76 (2) Protease and inhibitors/ECM
PLAUR Plasminogen activator, urokinase receptor   1.70 Protease and inhibitors/ECM
SERPINE1 PAI-1 plasminogen activator inhibitor type 1 5.80 (2) 3.74 (3) Protease and inhibitors/ECM
BMP1 Bone morphogenetic protein 1   2.29 Secreted factor
FSTL3 Follistatin-like 3 (secreted glycoprotein) 2.31 3.00 Secreted factor
IL11 Interleukin 11 2.78 2.13 (2) Secreted factor
JAG1 Jagged 1 (Alagille syndrome) 1.98 1.99 Secreted factor
LTBP2 Latent transforming growth factor-β binding protein 2 2.44 3.12 Secreted factor
LTBP3 Latent transforming growth factor-β binding protein 3   3.26 Secreted factor
STC1 Stanniocalcin 1 2.99 (2) 2.01 (3) Secreted factor
TGFB1 Transforming growth factor, beta 1 5.77 3.98 (2) Secreted factor
WNT5B Wingless-type MMTV integration site family, 5B 1.80 5.82 Secreted factor
CGB Chorionic gonadotropin, beta polypeptide 18.25 45.95 Secreted factor
ARHB RhoB 2.83 1.91 Signal transduction
ARHD ras homolog gene family, member D   9.26 Signal transduction
CSF1R Colony stimulating factor 1 receptor, (v-fms) oncogene   7.16 Signal transduction
EPHB2 EphB2 5.09 6.30 (4) Signal transduction
MADH7 MAD, mothers against decapentaplegic homolog 7 2.16 5.79 Signal transduction
MAPK13 Mitogen-activated protein kinase 13   2.28 Signal transduction
MAPK8IP3 Mitogen-activated protein kinase 8 interact. protein 3   2.02 Signal transduction
PIK3CD Phosphoinositide-3-kinase, catalytic, delta polypeptide   2.46 Signal transduction
RAB31 RAB31, member RAS oncogene family   1.82 Signal transduction
RALB v-ral simian leukemia viral oncogene homolog B   1.93 Signal transduction
SGNE1 Secretory granule, neuroendocrine protein 1   10.38 Signal transduction
SPEC1 Small protein effector 1 of Cdc42 1.92 1.97 Signal transduction
TMEPAI Transmembrane, prostate androgen induced RNA 7.85 9.08 Signal transduction
ABL1 v-abl Abelson murine leukemia viral oncogene 1   1.95 Signal transduction
NET1 Neuroepithelial cell transforming gene 1   2.25 (2) Signal transduction
PINK1 phosphatase and tensin homolog (PTEN) induced putative kinase 1   1.98 (2) Signal transduction
PORCN Likely ortholog of mouse porcupine homolog, PPN   2.49 Signal transduction
PTPRK Protein tyrosine phosphatase, receptor type, K 1.85 2.29 Signal transduction
JUN v-jun sarcoma virus 17 oncogene homolog (avian)   1.98 (2) Transcription factor
JUNB jun B proto-oncogene 2.01 8.34 Transcription factor
MONDOA Mlx interactor   2.26 Transcription factor
SOX4 SOX4 gene for SRY (sex determining region Y)-box 4   1.97 Transcription factor
BHLHB2 Basic helix-loop-helix domain containing, class B, 2 4.26 (2) 4.61 (2) Transcription factor
SNAI2 Snail homolog 2 (Drosophila)   2.37 Transcription factor
  1. a,b The primary sequence names and descriptions for the differentially regulated genes (defined as greater or equal to 1.7-fold changed with a p-value of < 0.01) were extracted using Rosetta Resolver. Genes from the dominant ontology classes are shown and thus genes with unknown function or those not in well represented ontology classes are not listed. The complete set of differentially expressed genes can be found in Additional files 6, 7, 8, 9. c Fold change in expression of the induced or repressed genes in the MDA-MB-231 CN cell line after a 24 h exposure to 2 ng/ml recombinant TGF-β1 compared to the diluent treated controls. The number in parentheses after the fold change indicates the number of affected elements that were averaged to calculate the fold difference. d Fold change in expression of the induced or repressed genes in the MDA-MB-231 H2 cell line after a 24 h exposure to 2 ng/ml recombinant TGF-β1 compared to the diluent treated controls. The number in parentheses to the right of the fold change indicates the number of affected elements that were averaged to calculate the fold difference. e The gene ontology annotation was curated from the Summary Function and GO fields downloaded from SOURCE [105].