Supplementary Information of "Guidelines for biomarker discovery in endometrium: Correcting for menstrual cycle bias reveals new uterine disorders associated genes"

<b>Table SII. Top uterine disorder biomarkers previously masked by the menstrual cycle effect. </b>Gene symbol, average expression, t-Student statistic, p-value, false discovery rate (FDR), fold change (FC) and absolute percentage of increased/decreased expression between cases and controls after differential expression analysis with menstrual cycle effect correction are provided for the top 20 (in terms of absolute FC) endometrial biomarkers of A) eutopic endometriosis (Burney2007, n=685), B) ectopic ovarian endometriosis (Hawkins2011, n=302), and C) recurrent implantation failure (Koot2016, n=30) that were previously masked by the menstrual cycle effect. Included new uterine disorder biomarkers (544 for eutopic endometriosis, 158 for ectopic ovarian endometriosis, and 27 for RIF) that were not previously reported in the original articles or in the databases Disgenet v.6 (Piñero <i>et al.</i>, 2019), Phenopedia v.6.2.3 (Yu <i>et al.</i>, 2010), and/or GeneCards v.4.14.0 (Stelzer <i>et al.</i>, 2016) are underlined.<b>Table SIII. Functional annotation for the newly discovered potential uterine disorder biomarkers. </b>For the new potential biomarkers of eutopic endometriosis (n=544) (B), ectopic endometriosis (n=158) (C) and RIF (n=27) (D) not previously reported in the literature, gene names, GeneCards description (Stelzer <i>et al.</i>, 2016), annotated GO biological processes, molecular functions and cellular components (Ashburner <i>et al</i>., 2000) and annotated KEGG pathways (Ogata <i>et al</i>., 1999) are indicated. For GO annotation, only experimental-evidenced GO-gene associations were included, a propagated GO version was used for considering the whole GO-tree structure, and annotated GO terms were filtered by those having more than five and less than 500 associated genes. Obtained GO and KEGG annotated terms were then grouped in broader functional categories (A). Table SIIIA shows, for each defined functional group, literature references supporting its role in the pathophysiology of endometriosis and/or RIF; together with the number of associated genes and gene names by study/uterine disorder. Keywords used in PubMed to search for functions altered in endometriosis and RIF patients included “endometriosis”, “RIF”, “recurrent implantation failure”, “function”, “pathway”, “gene ontology” and “KEGG”. GO, Gene Ontology. KEGG, Kyoto Encyclopedia of Genes and Genomes.