Potential bioactive compound and hub gene identification of endometrial carcinoma using systems biology

References

• Ashburner, M. (2000). Gene ontology: Tool for the unification of biology the gene ontology consortium*. http://www.flybase.bio.indiana.edu
   Google Scholar
• Bina, F., Soleymani, S., Toliat, T., Hajimahmoodi, M., Tabarrai, M., Abdollahi, M., & Rahimi, R. (2019). Plant-derived medicines for treatment of endometriosis: A comprehensive review of molecular mechanisms. Pharmacological Research, 139, 76–90. https://doi.org/10.1016/j.phrs.2018.11.008
   PubMed Web of Science ®Google Scholar
• Chen, J. J., Wang, S. J., Tsai, C. A., & Lin, C. J. (2007). Selection of differentially expressed genes in microarray data analysis. The Pharmacogenomics Journal, 7(3), 212–220. https://doi.org/10.1038/sj.tpj.6500412
   PubMed Web of Science ®Google Scholar
• Chin, C.-H., Chen, S.-H., Wu, H.-H., Ho, C.-W., Ko, M.-T., & Lin, C.-Y. (2014). cytoHubba: Identifying hub objects and sub-networks from complex interactome. BMC Systems Biology, 8 Suppl 4(Suppl 4), S11. https://doi.org/10.1186/1752-0509-8-S4-S11
   PubMedGoogle Scholar
• Di Cristofano, A., & Ellenson, L. H. (2007). Endometrial carcinoma. Annual Review of Pathology: Mechanisms of Disease, 2(1), 57–85. https://doi.org/10.1146/annurev.pathol.2.010506.091905
   PubMedGoogle Scholar
• Du Plessis, L., Skunca, N., & Dessimoz, C. (2011). The what, where, how and why of gene ontology-A primer for bioinformaticians. Briefings in Bioinformatics, 12(6), 723–735. https://doi.org/10.1093/bib/bbr002
   PubMed Web of Science ®Google Scholar
• Fan, J., Fu, A., & Zhang, L. (2019). Progress in molecular docking. Quantitative Biology, 7(2), 83–89. https://doi.org/10.1007/s40484-019-0172-y
   Google Scholar
• Fonseka, P., Pathan, M., Chitti, S. V., Kang, T., & Mathivanan, S. (2021). FunRich enables enrichment analysis of OMICs datasets. Journal of Molecular Biology, 433(11), 166747. https://doi.org/10.1016/j.jmb.2020.166747
   PubMed Web of Science ®Google Scholar
• Gomathi, D., Kalaiselvi, M., Ravikumar, G., Devaki, K., & Uma, C. (2015). GC-MS analysis of bioactive compounds from the whole plant ethanolic extract of Evolvulus alsinoides (L.) L. Journal of Food Science and Technology, 52(2), 1212–1217. https://doi.org/10.1007/s13197-013-1105-9
   PubMed Web of Science ®Google Scholar
• Griffith, M., Spies, N. C., Krysiak, K., McMichael, J. F., Coffman, A. C., Danos, A. M., Ainscough, B. J., Ramirez, C. A., Rieke, D. T., Kujan, L., Barnell, E. K., Wagner, A. H., Skidmore, Z. L., Wollam, A., Liu, C. J., Jones, M. R., Bilski, R. L., Lesurf, R., Feng, Y.-Y., … Griffith, O. L. (2017). CIViC is a community knowledgebase for expert crowdsourcing the clinical interpretation of variants in cancer. Nature Genetics, 49(2), 170–174. https://doi.org/10.1038/ng.3774
   PubMed Web of Science ®Google Scholar
• Hasnain, M. J. U., Shoaib, M., Qadri, S., Afzal, B., Anwar, T., Abbas, S. H., Sarwar, A., Talha Malik, H. M., & Tariq Pervez, M. (2020). Computational analysis of functional single nucleotide polymorphisms associated with SLC26A4 gene. PloS One, 15(1), e0225368. https://doi.org/10.1371/journal.pone.0225368
   PubMed Web of Science ®Google Scholar
• Hollingsworth, S. A., & Dror, R. O. (2018). Molecular dynamics simulation for all. Neuron, 99(6), 1129–1143. https://doi.org/10.1016/j.neuron.2018.08.011
   PubMed Web of Science ®Google Scholar
• Ilhan, M., Gürağaç Dereli, F. T., & Akkol, E. K. (2019). Novel drug targets with traditional herbal medicines for overcoming endometriosis. Current Drug Delivery, 16(5), 386–399. https://doi.org/10.2174/1567201816666181227112421
   PubMed Web of Science ®Google Scholar
• Johnson, Z. J., Krutkin, D. D., Bohutskyi, P., & Kalyuzhnaya, M. G. (2021). Metals and methylotrophy: Via global gene expression studies. Methods in Enzymology, 650, 185–213. https://doi.org/10.1016/bs.mie.2021.01.046
   PubMed Web of Science ®Google Scholar
• Karunamoorthi, K., Jegajeevanram, K., Vijayalakshmi, J., & Mengistie, E. (2013). Traditional medicinal plants: A source of phytotherapeutic modality in resource-constrained health care settings. Journal of Evidence-Based Complementary & Alternative Medicine, 18(1), 67–74. https://doi.org/10.1177/2156587212460241
   Google Scholar
• Liu, J., Wan, Y., Li, S., Qiu, H., Jiang, Y., Ma, X., Zhou, S., & Cheng, W. (2020). Identification of aberrantly methylated differentially expressed genes and associated pathways in endometrial cancer using integrated bioinformatic analysis. Cancer Medicine, 9(10), 3522–3536. https://doi.org/10.1002/cam4.2956
   PubMed Web of Science ®Google Scholar
• Meresman, G. F., Götte, M., & Laschke, M. W. (2021). Plants as source of new therapies for endometriosis: A review of preclinical and clinical studies. Human Reproduction Update, 27(2), 367–392. https://doi.org/10.1093/humupd/dmaa039
   PubMed Web of Science ®Google Scholar
• Otasek, D., Morris, J. H., Bouças, J., Pico, A. R., & Demchak, B. (2019). Cytoscape automation: Empowering workflow-based network analysis. Genome Biology, 20(1), 185. https://doi.org/10.1186/s13059-019-1758-4
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Shoichet BK, McGovern SL, Wei B, Irwin JJ. Lead discovery using molecular docking. Curr Opin Chem Biol. 2002 Aug;6(4):439–46. doi: 10.1016/s1367-5931(02)00339-3.
   Google Scholar
• Sousa, M., Pozniak, A., & Boffito, M. (2008). Pharmacokinetics and pharmacodynamics of drug interactions involving rifampicin, rifabutin and antimalarial drugs. The Journal of Antimicrobial Chemotherapy, 62(5), 872–878. https://doi.org/10.1093/jac/dkn330
   PubMed Web of Science ®Google Scholar
• Szklarczyk, D., Gable, A. L., Lyon, D., Junge, A., Wyder, S., Huerta-Cepas, J., Simonovic, M., Doncheva, N. T., Morris, J. H., Bork, P., Jensen, L. J., & Mering, C. V (2019). STRING v11: Protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Research, 47(D1), D607–D613. https://doi.org/10.1093/nar/gky1131
   PubMed Web of Science ®Google Scholar
• Wani, T. A., Zargar, S., & Hussain, A. (2022). Spectroscopic, thermodynamic and molecular docking studies on molecular mechanisms of drug binding to proteins. Molecules (Basel, Switzerland), 27(23), 8405. https://doi.org/10.3390/molecules27238405
   PubMed Web of Science ®Google Scholar