Gene Expressional Differences in MCF-7 vs. MCF-10A cells, Venn Groups
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1 Gene Expressional Differences in MCF-7 vs. MCF-10A cells, Venn Groups e k g b Smad target genes (48) l o n i a h m j d Transcription Factors, And Genes Regulating Developmental Processes (44) TGF Superfamily Cytokines (44) f c Adhesion and Extracellular Molecules (27) Minimum Fold expression values ->640, -320, -160, -80, -40, -20, -10, -5, -2.5, 0, 2.5, 5, 10, 20, 40, 80, 160, 320, 640< + Supplemental Fig. 1
2 Supplemental Table 1. Change of Basal Gene Expressional values in MCF-7 as compared to MCF-10A cell line. Fold Gene # /Position GeneBank Symbol Up/Down Regulation T-test p-value Description Venn Group a 01 /A01 NM_ ACVR Activin A receptor, type I 02 /A02 NM_ ACVR2A Activin A receptor, type IIA 03 /A03 NM_ ACVRL Activin A receptor type II-like 1 05 /A05 NM_ AMHR Anti-Mullerian hormone receptor, type II 16 /B04 NM_ BMPR1A Bone morphogenetic protein receptor, type IA 17 /B05 NM_ BMPR1B Bone morphogenetic protein receptor, type IB 36 /C12 NM_ GDF Growth differentiation factor 5 (cartilage-derived morphogenetic protein-1) 37 /D01 NM_ GDF Growth differentiation factor 6 38 /D02 NM_ GDF Growth differentiation factor 7 53 /E05 NM_ LEFTY Left-right determination factor 1 59 /E11 NM_ NODAL Nodal homolog (mouse) 77 /G05 NM_ TGFB Transforming growth factor, beta 2 78 /G06 NM_ TGFB Transforming growth factor, beta 3 80 /G08 NM_ TGFBR Transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kDa) 81 /G09 NM_ TGFBR Transforming growth factor, beta receptor II (70/80kDa) 82 /G10 NM_ TGFBR Transforming growth factor, beta receptor III (betaglycan, 300kDa) 83 /G11 NM_ TGFBRAP Transforming growth factor, beta receptor associated protein 1 Venn Group b NM_ BAMBI BMP and activin membrane-bound inhibitor homolog 06 /A06 (Xenopus laevis) 15 /B03 NM_ BMPER BMP binding endothelial regulator 19 /B07 NM_ CDC25A Cell division cycle 25A 21 /B09 NM_ CDKN2B Cyclin-dependent kinase inhibitor 2B (p15, inhibits CDK4) 22 /B10 NM_ CER Cerberus 1, cysteine knot superfamily, homolog (Xenopus laevis) 27 /C03 NM_ CST Cystatin C (amyloid angiopathy and cerebral hemorrhage) 31 /C07 NM_ FKBP1B FK506 binding protein 1B, 12.6 kda 42 /D06 NM_ ID Inhibitor of DNA binding 2, dominant negative helixloop-helix protein 58 /E10 NM_ NBL Neuroblastoma, suppression of tumorigenicity 1 Venn Group f NM_ GDF Growth differentiation factor 2 34 /C10 35 /C11 NM_ GDF Growth differentiation factor 3 54 /E06 NM_ LTBP Latent transforming growth factor beta binding protein 1 55 /E07 NM_ LTBP Latent transforming growth factor beta binding protein 2 56 /E08 NM_ LTBP Latent transforming growth factor beta binding protein 4 Venn Group g NM_ COL3A Collagen, type III, alpha 1 (Ehlers-Danlos syndrome 26 /C02 type IV, autosomal dominant) 29 /C05 NM_ ENG Endoglin (Osler-Rendu-Weber syndrome 1) 63 /F03 NM_ PLAU Plasminogen activator, urokinase 65 /F05 NM_ SERPINE Serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 1 79 /G07 NM_ TGFBI Transforming growth factor, beta-induced, 68kDa - 1 -
3 Venn Group h NM_ BMP Bone morphogenetic protein 3 (osteogenic) 10 /A10 11 /A11 NM_ BMP Bone morphogenetic protein 4 12 /A12 NM_ BMP Bone morphogenetic protein 5 13 /B01 NM_ BMP Bone morphogenetic protein 6 14 /B02 NM_ BMP Bone morphogenetic protein 7 (osteogenic protein 1) 18 /B06 NM_ BMPR Bone morphogenetic protein receptor, type II (serine/threonine kinase) 61 /F01 NM_ NR0B Nuclear receptor subfamily 0, group B, member 1 74 /G02 NM_ TGFB Transforming growth factor, beta 1 (Camurati- Engelmann disease) Venn Group i NM_ CDKN1A Cyclin-dependent kinase inhibitor 1A (p21, Cip1) 20 /B08 23 /B11 NM_ CHRD Chordin 28 /C04 NM_ DLX Distal-less homeobox 2 30 /C06 NM_ EVI Ecotropic viral integration site 1 32 /C08 NM_ FOS V-fos FBJ murine osteosarcoma viral oncogene homolog 39 /D03 NM_ GSC Goosecoid 40 /D04 NM_ HIPK Homeodomain interacting protein kinase 2 41 /D05 NM_ ID Inhibitor of DNA binding 1, dominant negative helixloop-helix protein 51 /E03 NM_ JUN V-jun sarcoma virus 17 oncogene homolog (avian) 52 /E04 NM_ JUNB Jun B proto-oncogene 57 /E09 NM_ MYC V-myc myelocytomatosis viral oncogene homolog (avian) 60 /E12 NM_ NOG Noggin 64 /F04 NM_ RUNX Runt-related transcription factor 1 (acute myeloid leukemia 1; aml1 oncogene) 66 /F06 NM_ SMAD SMAD, mothers against DPP homolog 1 (Drosophila) 67 /F07 NM_ SMAD SMAD, mothers against DPP homolog 2 (Drosophila) 68 /F08 NM_ SMAD SMAD, mothers against DPP homolog 3 (Drosophila) 69 /F09 NM_ SMAD SMAD, mothers against DPP homolog 4 (Drosophila) 70 /F10 NM_ SMAD SMAD, mothers against DPP homolog 5 (Drosophila) 71 /F11 NM_ SMURF SMAD specific E3 ubiquitin protein ligase 1 72 /F12 NM_ SOX SRY (sex determining region Y)-box 4 84 /G12 NM_ TGIF TGFB-induced factor (TALE family homeobox) 76 /G04 NM_ TSC22D TSC22 domain family, member 1 Venn Group k NM_ IL Interleukin 6 (interferon, beta 2) 45 /D09 49 /E01 NM_ ITGB Integrin, beta 5 50 /E02 NM_ ITGB Integrin, beta 7 62 /F02 NM_ PDGFB Platelet-derived growth factor beta polypeptide (simian sarcoma viral (v-sis) oncogene homolog) Venn Group l NM_ STAT Signal transducer and activator of transcription 1, 73 /G01 91kDa Venn Group m NM_ AMH Anti-Mullerian hormone 04 /A04 08 /A08 NM_ BMP Bone morphogenetic protein 1 09 /A09 NM_ BMP Bone morphogenetic protein 2 46 /D10 NM_ INHA Inhibin, alpha 47 /D11 NM_ INHBA Inhibin, beta A (activin A, activin AB alpha polypeptide) 48 /D12 NM_ INHBB Inhibin, beta B (activin AB beta polypeptide) Venn Group n 07 /A07 NM_ BGLAP Bone gamma-carboxyglutamate (gla) protein (osteocalcin) 24 /B12 NM_ COL1A Collagen, type I, alpha 1-2 -
4 25 /C01 NM_ COL1A Collagen, type I, alpha 2 33 /C09 NM_ FST Follistatin Venn Group o NM_ IGF Insulin-like growth factor 1 (somatomedin C) 43 /D07 44 /D08 NM_ IGFBP Insulin-like growth factor binding protein 3 75 /G03 NM_ TGFB1I Transforming growth factor beta 1 induced transcript 1 House-keeping gene controls NM_ B2M Beta-2-microglobulin H01 H02 NM_ HPRT Hypoxanthine phosphoribosyltransferase 1 (Lesch- Nyhan syndrome) H03 NM_ RPL13A Ribosomal protein L13a H04 NM_ GAPDH Glyceraldehyde-3-phosphate dehydrogenase H05 NM_ ACTB Actin, beta The sub-groups that contained no genes (c, e, j, d in Figure 3) are not listed. The significant negative values are blue and the positive change is pink. The relevant p-values are highlighted in red
5 Genes MCF-7/MCF-10A Un-treated controls Table 2 SuperArray Validation with TaqMan Assay (Fold Change) Treatment CII LAM TGF MCF-10A MCF-7 MCF-10A MCF-7 MCF-10A MCF-7 SA TaqMan SA TaqMan SA TaqMan SA TaqMan SA TaqMan SA TaqMan SA TaqMan BMP BMP CDKN2B FST SERPINE PDGFB N/A N/A N/A N/A PLAU N/A N/A N/A N/A TGFBR N/A N/A 1.20 N/A 1.46 N/A TGFBR N/A N/A N/A N/A N/A 1.21 N/A TGFBR N/A N/A N/A 1.74 N/A N/A N/A TGFBI N/A 1.06 N/A N/A N/A 1.36 N/A 1.12 N/A TaqMan Probes Used: BMP2 BMP7 CDKN2B FST SERPINE1 PDGFB PLAU TGFBR1 TGFBR2 TGFBR3 TGFBI Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1 Hs _m1
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