Supplementary data for:

MOLECULAR EFFECTS OF GENISTEIN ON THE URETHRA

Ashley E. Ross, Luigi Marchionni, Timothy M. Philips, Rebecca M. Miller, Paula J. Hurley, Brian W. Simons, Amirali H. Salmasi, Anthony J. Schaeffer, John P. Gearhart, Edward M. Schaeffer





The "Supplementary Methods" section can be downloaded here:

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    "Supplementary Tables" can be downloaded here:

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    DIFFERENTIAL GENE EXPRESSION

    Below is the lists of differentially expressed genes in the developing urethra of mice upon gestational exposure to endocrine disruptors (genistein). All the results were obtained using a generalized linear model approach, using a single-channel design, and by applying an empirical Bayesian method to moderate variance across genes.

    The list of genes differentially expressed in the urethra upon gestational exposure to different levels of genistein is reported below. The comparison was performed between high levels of genistein and normal diet, using the normal diet as the denominator to compute the fold-change.

    FileName Description
    Urethra HIGH genistein vs NORMAL diet HIGH genistein diet versus LOW Genistein diet coefficient;
    top 2.5% genes by adjusted P-value

    Columns in the html file can be sorted by clicking the column header. The legend to the table headers is below:

    ProbeName: Agilent Probe Identifier
    logFC: Logarithmic transformation (base 2) of the fold-change between groups
    AveExpr: Logarithmic transformation (base 2) of the average expression for the group
    t: Moderated t-statistics
    P.value: Unadjusted P value
    adj.P.Val: Adjusted P value with the Benjamini-Hochberg method
    B: B-statistics, log odds
    EGID: Entrez Gene Identifier, linked to the NCBI ENTREZ Gene database
    SYMBOL: Gene Symbol
    GENENAME: Official Gene Name
    UNIGENE: Unigene Cluster Identifier, linked to the NCBI Unigene database
    ENSEMBL: ENSEMBL Gene Identifier, linked to the ENSEMBL database
    MGI: MGI Accession number, linked to the MGI database





    ANALYSIS OF FUNCTIONAL ANNOTATION

    Analysis of Functional Annotation (AFA) results for the comparison between high and normal genistein gestational exposure. This analysis is conceptually analogous to Gene Set Enrichment Analysis (GSEA). Functional Gene Sets from various sources (i.e. GO, KEGG, Molecular signature database,SMD,PubMed, and so on) were used and their description is reported.

    FileName Description
    Access results from AFA ANALYSIS OF FUNCTIONAL ANNOTATION





    DOWNLOAD RAW DATA

    Raw gene expression data can be downloaded at the link below

    FileName Description
    Download Tarbal archived of the raw gene expression data