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

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

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 12: of The molecular landscape of premenopausal breast cancer

Supplementary methods. This file contains additional details of the analyses. (DOCX 36 kb

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

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

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

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

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

Additional file 1: Figure S1. of Alcohol consumption and breast tumor gene expression

ESR1, PGR, ERBB2 mRNA expression by IHC ER, PR, and HER2, respectively, in the NHS and the NHSII. (PDF 273 kb

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

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

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

<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

The most significant SNPs in the transport pathway genes and risk of EOC by histology, invasiveness, and race/ethnicity¹.

<p>¹ INV: all invasive EOC combined; LMP: low malignant potential / borderline tumors; SER: serous; CC: clear cell; End: endometrioid; Muc: mucinous. Statistically significant associations are indicated in bold (P<0.05). Data format is the following: OR (95% CI); p-value; FDR q-value (white-European women). Only significant FDRs (q<0.2) are shown (<i>HEPH</i>: INV and SER<i>; UGT1A</i>: End).</p><p>The most significant SNPs in the transport pathway genes and risk of EOC by histology, invasiveness, and race/ethnicity<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0128106#t001fn001" target="_blank">¹</a>.</p