{"paper_id":"ba85c548-6ce2-4f79-8c1e-50b75ffac4a2","body_text":"Abstract\nEndometriosis (EM) is a gynecological condition known by the manifestation of endometrium alike soft tissue external to the usual place affecting up to 10% of all womenfolk in the reproductively active stage. However, the pathological process of endometriosis is not identified fully. The study aims to investigate the genes associated with the progression of endometriosis and its pathways using bioinformatics tools and techniques. The gene expression profile of three sets was retrieved, and bioinformatics data analysis was carried out for the microarray samples using GEO, DAVID, and STICH. Differently expressed genes (DEGs) refer to genes that exhibit significant changes in their expression levels between different conditions or groups, such as between different cell types, treatments, disease states, or developmental stages. DEG was determined based on a significant cutoff resulting in 298 unique elements based on the GEO Venn diagram map. DAVID (database for annotation, visualization, and integrated discovery) helps understand the biological significance of the data by identifying overrepresented biological terms, pathways, and functional annotations among a set of genes or proteins of interest. DAVID analysis revealed positively and negatively associated genes and followed by target proteins. DAVID is helpful for getting results of molecular mechanisms and pathways associated with DEGs. The gene expression studies showed that the m-RNA expression of all the genes was upregulated in the PA1 cell line. The present study identified five genes (COMT, CYP19A1, GALT, LTA, and STAR) from 298 unique DEGs using microarray data analysis, and 5 protein targets were also identified that were linked with EM. The study concludes that this information may provide a bridging gap in understanding the progression of endometriosis.\nSimilar content being viewed by others\nData availability\nThe datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request.\nAbbreviations\n- COMT:\n-\nCatechol-O-methyltransferase\n- DAVID:\n-\nDatabase for annotation, visualization, and integrated discovery\n- DEGs:\n-\nDifferently expressed genes\n- EM:\n-\nEndometriosis\n- EAOC:\n-\nEndometriosis-associated and non-endometriosis-associated (non-EAOC)\n- GEO:\n-\nGene Expression Omnibus\n- GALT:\n-\nGut-associated lymphoid tissue\n- KEGG:\n-\nKyoto encyclopedia of genes and genomes\n- miRNAs:\n-\nMicro-RNAs\n- PMSF:\n-\nPhenylmethylsulfonyl fluoride\n- PPI:\n-\nProtein-protein interaction\n- qPCR:\n-\nQuantitative polymerase chain reaction\n- RIPA:\n-\nRadioimmunoprecipitation assay buffer\n- WGCNA:\n-\nWeighted gene co-expression network analysis\n- WHO:\n-\nWorld Health Organization\nReferences\nRahal, D., Andrade, F., & Nisihara, R. 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All authors contributed to the study conception and design, material preparation, the experiments, data collection, and analysis. All authors wrote the first draft of the manuscript and commented on previous versions of the manuscript. All authors read and approved the final manuscript.\nCorresponding author\nEthics declarations\nEthics Approval\nNot applicable.\nConflict of Interest\nThe authors declare no competing interests.\nAdditional information\nPublisher's Note\nSpringer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.\nRights and permissions\nSpringer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.\nAbout this article\nCite this article\nZhang, Z., Singh, S.P. A Study on the Analysis of Important Gene Networks and Pathways Involved in Progression of Endometriosis to Ovarian Endometrioma Cyst. Appl Biochem Biotechnol 196, 4352–4365 (2024). https://doi.org/10.1007/s12010-023-04778-2\nAccepted:\nPublished:\nVersion of record:\nIssue date:\nDOI: https://doi.org/10.1007/s12010-023-04778-2","source_license":"CC0","license_restricted":false}