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Table 1 Dominant transforming growth factor-β gene signatures in the luminal MCF-7 CN and MCF-7 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 MCF-7 CNc Fold Δ MCF-7 H2d Gene ontologye
TGF-β induced genes     
   BCL3 B-cell chronic lymphocytic Leukemia (CLL)/lymphoma 3 1.70   Cell cycle
   BACE Beta-site amyloid precursor protein (APP)-cleaving enzyme 2.86   ECM/adhesion
   CD59 CD59 antigen p18-20 1.74 (3)   ECM/adhesion
   CDH11 Cadherin 11, type 2, OB-cadherin (osteoblast) 1.94   ECM/adhesion
   COL18A1 Collagen, type XVIII, alpha 1 1.91   ECM/adhesion
   COL5A1 Collagen, type V, alpha 1 5.01 (2) 4.22 (2) ECM/adhesion
   IGSF4 Immunoglobulin superfamily, member 4 1.94 1.81 ECM/adhesion
   SCARB1 Scavenger receptor class B, member 1 1.77   ECM/adhesion
   SPOCK Sparc/osteonectin (testican) 8.23   ECM/adhesion
   THBS1 Thrombospondin 1 2.31 (3)   ECM/adhesion
   BMP7 Bone morphogenetic protein 7 (osteogenic protein 1) 2.05   Secreted factor
   IGFBP5 Insulin-like growth factor binding protein 5 4.56   Secreted factor
   MSMB microseminoprotein, beta- 11.19 (2) 3.65 (2) Secreted factor
   CBFA2T3 Core-binding factor, runt domain, alpha subunit 2 2.06   Transcription factor
   DZIP3 Zinc finger DAZ interacting protein 3 1.93   Transcription factor
   ELK3 Sapiens cDNA: FLJ22425 fis, clone HRC08686 1.90   Transcription factor
   FOXO1A Forkhead box O1A (rhabdomyosarcoma) 3.45 (2)   Transcription factor
   MADH3 MAD, mothers against decapentaplegic homolog 3 4.77   Transcription factor
   NRBP Nuclear receptor binding protein 2.12   Transcription factor
   PLU-1 Putative DNA/chromatin binding motif 1.75 (2)   Transcription factor
   SOLH Small optic lobes homolog (Drosophila) 1.86   Transcription factor
   TGIF Transforming growth factor beta (TGFB)-induced factor (TALE family homeobox) 1.70   Transcription factor
   TIEG Transforming growth factor beta (TGFB) inducible early growth response 1.77   Transcription factor
TGF-β repressed genes     
   BIRC5 Baculoviral inhibitor of apoptosis (IAP) repeat-containing 5 (survivin) -3.04   Apoptosis
   CCNA2 Cyclin A2 -2.18   Cell cycle
   CCNB1 Cyclin B1 -1.99   Cell cycle
   CCNB2 Cyclin B2 -1.94   Cell cycle
   CCNE2 Cyclin E2 -2.03   Cell cycle
   CDC2 Cell division cycle 2, G1 to S and G2 to M -2.62 (2) -1.77 (2) Cell cycle
   CDC20 CDC20 cell division cycle 20 homolog (S. cerevisiae) -2.10   Cell cycle
   CDC25C Cell division cycle 25C -2.02   Cell cycle
   CDKN2C Cyclin-dependent kinase inhibitor 2C (p18, inhibits CDK4) -2.59   Cell cycle
   CDKN3 Cyclin-dependent kinase inhibitor 3 -2.66   Cell cycle
   CKS1B CDC28 protein kinase regulatory subunit 1B -1.96   Cell cycle
   CKS2 CDC28 protein kinase regulatory subunit 2 -1.70   Cell cycle
   MKI67 Antigen identified by monoclonal antibody Ki-67 -2.26 (2) -2.84 Cell cycle
   MPHOSPH9 M-phase phosphoprotein 9 -1.86   Cell cycle
   NEK2 NIMA (never in mitosis gene a)-related kinase 2 -2.93   Cell cycle
   ASPM asp (abnormal spindle)-like, microcephaly associated -2.48   Chromosome reg.
   BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog -2.08 -1.72 Chromosome reg.
   BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog β -1.78   Chromosome reg.
   CENPA Centromere protein A, 17 kDa -2.53   Chromosome reg.
   CENPE Centromere protein E, 312kDa -9.38 -4.87 Chromosome reg.
   CENPF Centromere protein F, 350/400 kDa (mitosin) -2.42   Chromosome reg.
   CNAP1 Chromosome condensation-related Structural maintenance of chromosomes (SMC)-associated protein 1 -1.99   Chromosome reg.
   ESPL1 Extra spindle poles like 1 (S. cerevisiae) -2.62   Chromosome reg.
   HCAP-G Chromosome condensation protein G -2.29 (2) -1.90 Chromosome reg.
   HEC Highly expressed in cancer, rich in leucine heptad repeats -4.35 -2.32 Chromosome reg.
   PRC1 Protein regulator of cytokinesis 1 -2.23   Chromosome reg.
   SMC2L1 SMC2 structural maintenance of chromosomes 2-like 1 -3.27 -1.70 Chromosome reg.
   ZWINT ZW10 interactor -1.75   Chromosome reg.
   BARD1 BRCA1 associated RING domain 1 -1.92   DNA metabolism
   BRIP1 BRCA1 interacting protein C-terminal helicase 1 -1.71   DNA metabolism
   CDT1 DNA replication factor -1.70   DNA metabolism
   PIR51 RAD51-interacting protein -2.17   DNA metabolism
   POLD1 Polymerase (DNA directed), delta 1, catalytic subunit -2.68   DNA metabolism
   POLE2 Polymerase (DNA directed), epsilon 2 (p59 subunit) -1.78   DNA metabolism
   PRIM1 Primase, polypeptide 1, 49 kDa -1.76   DNA metabolism
   RAD51C RAD51 homolog C (S. cerevisiae) -1.72   DNA metabolism
   RFC4 Replication factor C (activator 1) 4, 37 kDa -1.72   DNA metabolism
   TOP2A Topoisomerase (DNA) II alpha 170 kDa -2.68 (2)   DNA metabolism
   ID1 Inhibitor of DNA binding 1, dominant negative HLH protein -1.74   Transcription factor
   MXD3 MAX dimerization protein 3 -22.10   Transcription factor
   MYBL1 v-myb myeloblastosis viral oncogene homolog-like 1 -2.09   Transcription factor
   MYBL2 v-myb myeloblastosis viral oncogene homolog-like 2 -2.07   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 2, 3, 4, 5. c Fold change in expression of the induced or repressed genes in the MCF-7 CN cell line after a 24 h exposure to 2 ng/ml recombinant transforming growth factor (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 MCF-7 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].