en Clinical Physiology/Pharmacology Clinical Physiology/Pharmacology Clinical research article Clinical research article <p><span style="font-size:12px;"><span style="font-family:Arial;"><strong>Introduction:</strong> Endometriosis (EMS) is a highly prevalent gynecological disorder with substantial health consequences, affecting as many as 10% of women in their reproductive years. Although EMS is widespread, its intricate origin and pathophysiology are not well understood. This study investigated the molecular characteristics of EMS by examining the expression patterns of long noncoding RNAs (lncRNAs), microRNAs (miRNAs), and genes linked to the condition.<br /> <strong>Methods: </strong>The study used publicly accessible datasets, namely RNA-seq data for long non-coding RNAs (GSE105764), miRNA expression data (GSE105765), and gene expression data (GSE12768), to compare samples of ectopic and eutopic endometrial samples. The study conducted differential expression analysis, pathway enrichment analyses, protein-protein interaction network creation, and hub gene identification to uncover the molecular markers linked to EMS.&nbsp;<br /> <strong>Results:</strong> The investigation identified substantial dysregulation of lncRNAs, miRNAs, and genes in endometriotic tissues compared with the control eutopic endometrium. Hub genes, including CDH1, ESR1, GATA4, PGR, FOXA2, EPCAM, APOA1, BDNF, FGFR2, and PAX2, dominate the molecular landscape. miR-6500-3p has been identified as a pivotal regulator that influences the expression of seven essential genes. Pathway enrichment analysis identified biological processes, including embryonic organ morphogenesis, immunological response, and medication metabolism. Exploring lncRNA-mediated regulatory axes, particularly H19 and MIR600HG, suggests complex networks that may clarify the molecular underpinnings of EMS.<br /> <strong>Conclusion:</strong> This thorough investigation offers significant insight into the molecular pathways underlying EMS. Hub genes and regulatory miRNAs, including miR-6500-3p, have been identified as prospective targets for therapeutic interventions. Pathway enrichment studies provide a more comprehensive understanding of the biological processes implicated in EMS, indicating new possibilities for therapeutic interventions.</span></span></p> Endometriosis, lncRNAs, miRNAs, Hub Genes, Bioinformatics 155 170 http://ppj.phypha.ir/browse.php?a_code=A-10-2375-1&slc_lang=en&sid=1 Shahrzad Zhaeentan zhaeentan.shahrzad@yahoo.com 3200319475328460037746 3200319475328460037746 No Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Fardin Amidi amidifardin@yahoo.com 3200319475328460037747 3200319475328460037747 No Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Ashraf Moini moeinias@tums.ac.ir 3200319475328460037748 3200319475328460037748 No Department of Gynecology and Obstetrics, Arash Women’s Hospital, Tehran University of Medical Sciences, Tehran, Iran Seyed Danial Mohammadi drsdmohammadi@gmail.com 3200319475328460037749 3200319475328460037749 No Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Aligholi Sobhani sobhania@tums.ac.ir 3200319475328460037750 3200319475328460037750 No Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran Masoomeh Nataj Majd mnataj54@yahoo.com 3200319475328460037751 3200319475328460037751 No Department of Infertility, Arash Women’s Hospital, Tehran University of Medical Sciences, Tehran, Iran Mahshad khodarahmian ma.khodarahmian@gmail.com 3200319475328460037752 3200319475328460037752 Yes Department of Anatomy, School of Medicine, Tehran University of Medical Sciences, Tehran, Iran