{"owner": "ArrayExpress Uploader", "pop_total": 0, "species": "human", "factors": [{"GSM1419673": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "1.5", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419672": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM141967": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "46.9", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419670": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "5.9", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419669": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "169", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419668": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "155", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419667": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "38.3", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419666": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "4.8", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419665": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "2.1", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419664": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "3.6", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419663": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "9.7", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419662": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "3.76", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM141966": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.33", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419660": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0.36", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419659": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.61", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419658": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.36", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419657": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0.34", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419656": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.35", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419655": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.34", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419654": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.35", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419653": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0.53", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419652": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0.34", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM141965": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "1.4", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419650": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "27", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419649": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "84.5", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419648": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.33", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419647": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "0.34", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419646": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "110", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419645": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.34", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "Her2"}}, {"GSM1419644": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "0.33", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419643": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "9.62", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419642": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.64", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM141964": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "4.5", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419640": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.45", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419639": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.12", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419638": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.86", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419637": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "37.01", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "Her2"}}, {"GSM1419636": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "1.25", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419635": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "93.3", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419634": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.93", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419633": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "201.02", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419632": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "2.47", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM141963": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "6.89", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419630": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "387.86", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419629": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "6.45", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419628": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "3.31", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419627": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.32", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419626": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "1.15", "ER.STATUS": "N", "PREDICTED MOLECULAR SUBTYPE": "basal"}}, {"GSM1419625": {"TREATMENT": "placebo", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "1.29", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumA"}}, {"GSM1419624": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "post", "PLASMA GENISTEIN NG/ML": "51.61", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}, {"GSM1419623": {"TREATMENT": "soy", "MENOPAUSAL STATUS": "pre", "PLASMA GENISTEIN NG/ML": "6.26", "ER.STATUS": "P", "PREDICTED MOLECULAR SUBTYPE": "LumB"}}], "id": 1995, "ownerprofile_id": "arrayexpress_sid", "platform": 4, "summary_wrapped": "Background   There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy...", "geo_gse_id": "E-GEOD-58792", "owner_profile": "/profile/8773/arrayexpressuploader", "factor_count": 5, "sample_count": 51, "tags": ["breast", "breast cancer", "cancer", "cell", "genome", "protein"], "lastmodified": "Dec.12, 2014", "is_default": false, "geo_gds_id": "", "slug": "effects-of-soy-supplementation-on-gene-expression", "geo_id_plat": "E-GEOD-58792_A-AFFY-44", "name": "Effects of soy supplementation on gene expression in breast cancer", "created": "Jul.10, 2014", "summary": "Background   There are conflicting reports on the impact of soy on breast carcinogenesis. This study examines the effects of soy supplementation on breast cancer-related genes and pathways.  Methods   Women (n = 140) with early-stage breast cancer were randomized to soy protein supplementation (n = 70) or  placebo (n = 70) for 7 to 30 days, from diagnosis until surgery. Adherence was determined by plasma isoflavones:  genistein and daidzein. Gene expression changes were evaluated by NanoString inin pre- and post-treatment  tumor tissue. Genome-wide expression analysis was performed on post-treatment tissue. Proliferation (Ki67) and  apoptosis (Cas3) were assessed by immunohistochemistry.  Results   Plasma isoflavones rose in the soy group (two-sided Wilcoxon rank-sum test, P < .001) and did not change in  the placebo group. In paired analysis of pre- and post-treatment samples, 21 genes (out of 202) showed altered  expression (two-sided Student\u2019s t-test, P < .05). Several genes including FANCC and UGT2A1 revealed different  magnitude and direction of expression changes between the two groups (two-sided Student\u2019s t-test, P < .05).  A high-genistein signature consisting of 126 differentially expressed genes was identified from microarray analysis  of tumors. This signature was characterized by overexpression (>2 fold) of cell cycle transcripts, including  those which promote cell proliferation, such as FGFR2, E2F5, BUB1, CCNB2, MYBL2, CDK1, and CDC20 (P < .01).  Soy intake did not result in statistically significant changes in Ki67 or Cas3.  Conclusions   Gene expression associated with soy intake and high plasma genistein define a signature characterized by overexpression  of FGFR2 and genes that drive cell cycle and proliferation pathways. These findings raise the concerns  that in a subset of women soy could adversely affect gene expression in breast cancer. Genome-wide expression analysis was performed on breast cancer tissue from women following treatment with soy (n=28) or placebo (n=23).", "source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-58792", "sample_source": "http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-58792/samples/"}