11 research outputs found

    Additional file 7: of The molecular landscape of premenopausal breast cancer

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    PARADIGM analysis in The Cancer Genome Atlas (TCGA). Table S1. Pathways detected by gene set enrichment analysis (GSEA) with input of gene expression and copy number variation data for the PARADIGM algorithm. The nine columns correspond to the pathway name, size of the pathway, Enrichment score (ES) score, Normalized enrichment score (NES) score, nominal p value, false discovery rate (FDR) q value, Family-wise error rate (FWER) p value, and leading edge (typical GSEA output). Table S2. Pathways detected by GSEA with input of gene expression, copy number variation and methylation data for the PARADIGM algorithm. The nine columns correspond to the pathway name, the size of pathway, ES score, NES score, nominal p value, FDR q value, FWER p value, and leading edge (typical GSEA output). (XLSX 88 kb

    Additional file 11: of The molecular landscape of premenopausal breast cancer

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    Gene list for clustering premenopausal (preM) estrogen receptor-positive (ER+) tumors. Table S1. Gene list selected by sparse k-means algorithm in The Cancer Genome Atlas (TCGA) data. Table S2. Genes selected based on TCGA data that are also in the Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) data for validation. Table S3. Fixed number of genes (n = 21), gene list being selected from sparse k-means in TCGA. Table S4. Gene list selected by semi-supervised algorithm in METABRIC. Table S5. Fixed number of genes (n = 21), gene list being selected by semi-supervised algorithm in TCGA. Table S6. Genes (n = 28) in the LumA cluster that are significantly different between clusters 1 and 3. (XLSX 37 kb

    Additional file 2: Table S1. of Alcohol consumption and breast tumor gene expression

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    Comparison of study population characteristics in the NHS/NHSII and TCGA. Table S2. Characteristics of invasive breast cancer cases by recent alcohol consumption in the TCGA. Table S3. Top 10 ranked differentially expressed probes by recent alcohol consumption in the NHS and the NHSII. Table S4. Enriched gene sets (FDR 0.05–0.1) by recent alcohol consumption in ER+ tumors in the NHS and the NHSII. Table S5. Enriched gene sets (FDR 0.05–0.1) by recent alcohol consumption in ER- tumors in the NHS and the NHSII. Table S6. Enriched gene sets by alcohol consumption in stage II/III ER+ tumors in the NHS and the NHSII. (DOCX 56 kb

    Additional file 3: Figure S2. of Alcohol consumption and breast tumor gene expression

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    Differentially expressed probes (N = 25,979) by alcohol consumption in the NHS and the NHSII. The top four figures show recent alcohol intake > 0 - < 10 vs. 0 g/day and the bottom four figures show recent alcohol intake 10+ vs. 0 g/day. (PDF 1418 kb

    Association of rs2256787 in the <i>ARHGEF10L</i> gene with invasive endometrioid EOC risk by study site and combined.

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    <p>Squares represent the estimated per-allele odds ratio (OR) and are proportional to sample size for each study; lines indicate its 95% confidence interval (CI); source indicates contributing study;[<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0197561#pone.0197561.ref011" target="_blank">11</a>] MAF, control minor allele frequency; PVal, per-allele p-value adjusted for age, site, and principal components to account for residual differences in European ancestry.</p

    Association of variants in small GTPase genes with epithelial ovarian cancer risk (p-value<10<sup>−4</sup>) and functional annotation.

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    <p>Association of variants in small GTPase genes with epithelial ovarian cancer risk (p-value<10<sup>−4</sup>) and functional annotation.</p

    Top SNPs associated with SER EOC across racial groups.

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    <p><sup>1</sup> MAF, minor allele and its frequency</p><p><sup>2</sup> p-value <0.05 are in bold</p><p><sup>3</sup> Odds ratio, 95% confidence interval</p><p>Top SNPs associated with SER EOC across racial groups.</p
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