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Journal articles on the topic 'DAVID database'

Author: Grafiati

Published: 4 June 2025

Last updated: 1 August 2025

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1

Yu, Cheng, Liting Qian, Ying Chen, Jing Guan, Shuang Jiang, and Danning Song. "Study on the Mechanism of Coptis Chinensis in the Treatment of Diabetic Nephropathy Based on Network Pharmacology." BIO Web of Conferences 60 (2023): 01009. http://dx.doi.org/10.1051/bioconf/20236001009.

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To investigate the therapeutic effects of Coptis chinensis on diabetic nephropathy using systematic pharmacological techniques. The TCMSP database was used to search the main components and related targets of Coptis chinensis; the GeneCards and CTD databases were used to screen the disease targets of diabetic nephropathy, and the intersection of the targets and disease targets was taken and plotted in Venn diagram; the target protein interaction (PPI) network was constructed from STRING database; the DAVID 6.8 online tool was used to GO and KEGG enrichment analyses were performed using DAVID 6

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Barker, Bryce, Lara Lamb, and Tiina Manne. "Baikaboria Ossuary and the origins of the Kesele Clan, Upper Kikori River, Papua New Guinea." Journal of Pacific Archaeology 7, no. 1 (2016): 89——105. https://doi.org/10.5281/zenodo.6395743.

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A growing body of archaeological research in the western Gulf of Papua and its associated river systems has high- lighted the dynamic nature of occupation over the last few thousand years (Rhoads 1983; David 2008; David et al. 2010; McNiven et al. 2010; Barker et al. 2012; Barker et al. 2015; David et al. 2015). For example, it has been posited that the articulating stone-sago-pottery production systems and trade relations between the upper, middle and lower Kikori River effected regional polities, including marking the beginning of the social system which produced the

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Roberts, David. "Making the Word Count: towards an Analytical Database of Theatre Reviews." New Theatre Quarterly 15, no. 4 (1999): 332–38. http://dx.doi.org/10.1017/s0266464x00013269.

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Reviews are an indispensable resource for the theatre historian – records not only of individual productions and performances but of broader cultural attitudes. However, the few attempts to account for the review as a form are compromised by outmoded models both of authorship and, in particular, of language itself. This article describes the rationale, development, functionality, and initial results of an electronic database of theatre reviews which permits analysis of the form according to the principles of corpus linguistics. Such an approach, argues David Roberts, can track across a large b

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Soares, Mariza de Carvalho. "O COMÉRCIO “PORTUGUÊS/BRASILEIRO” DE ESCRAVOS NO TRANSATLANTIC SLAVE TRADE DATABASE." Almanack, no. 22 (August 2019): 551–68. http://dx.doi.org/10.1590/2236-463320192211.

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Resumo Este artigo é a versão escrita dos meus comentários orais ao texto de David Eltis intitulado “Capitalism and the Transatlantic Slave Trade: some broader implications of the intrusion of the Northern Europeans” apresentado por ocasião do Forum Almanack 2019 que tratou do comércio atlântico de escravos a partir dos dados recentes do The Transatlantic Slave Trade Database. Meus comentários enfocaram a construção do Database e a metodologia adotada pela equipe diretora do Database para sua expansão ao longo dos 20 anos que sucederam a divulgação dos primeiros resultados.

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Dickson, Kerim E., Landon T. Marston, and David A. Dzombak. "Editorial Perspectives: the need for a comprehensive, centralized database of interbasin water transfers in the United States." Environmental Science: Water Research & Technology 6, no. 3 (2020): 420–22. http://dx.doi.org/10.1039/d0ew90005b.

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Renaudie, Johan, David B. Lazarus, and Patrick Diver. "NSB (Neptune Sandbox Berlin): An expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy." Palaeontologia Electronica 23, no. 1 (2020): 1–28. https://doi.org/10.26879/1032.

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Renaudie, Johan, Lazarus, David B., Diver, Patrick (2020): NSB (Neptune Sandbox Berlin): An expanded and improved database of marine planktonic microfossil data and deep-sea stratigraphy. Palaeontologia Electronica (a11) 23 (1): 1-28, DOI: 10.26879/1032, URL: http://dx.doi.org/10.26879/1032

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Pierrat, Benjamin, Thomas Saucède, Alain Festeau, and Bruno David. "Antarctic, Sub-Antarctic and cold temperate echinoid database." ZooKeys 204 (June 25, 2012): 47–52. https://doi.org/10.3897/zookeys.204.3134.

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This database includes spatial data of Antarctic, Sub-Antarctic and cold temperate echinoid distribution (Echinodermata: Echinoidea) collected during many oceanographic campaigns led in the Southern Hemisphere from 1872 to 2010. The dataset lists occurrence data of echinoid distribution south of 35°S latitude, together with information on taxonomy (from species to genus level), sampling sources (cruise ID, sampling dates, ship names) and sampling sites (geographic coordinates and depth). Echinoid occurrence data were compiled from the Antarctic Echinoid Database (David et al., 2005a), which in

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Liao, Pan, Shuzhen Han, and Honglan Qu. "Expression, Prognosis, and Immune Infiltrates Analyses of E2Fs in Human Brain and CNS Cancer." BioMed Research International 2020 (December 15, 2020): 1–17. http://dx.doi.org/10.1155/2020/6281635.

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Objective. We investigated the expression patterns, potential functions, unique prognostic value, and potential therapeutic targets of E2Fs in brain and CNS cancer and tumor-infiltrating immune cell microenvironments. Methods. We analyzed E2F mRNA expression levels in diverse cancer types via Oncomine and GEPIA databases, respectively. Moreover, we evaluated the prognostic values using GEPIA database and TCGAportal database and the correlation of E2F expression with immune infiltration and the correlation between immune cell infiltration and GBM and LGG prognosis via TIMER database. Then, cBio

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Li, Ruochen, Mingxiao Wang, Jin Tian, Minghui Liu, Gaigai Li, and Xun Zhou. "Exploration of kiwi root on non-small cell lung cancer based on network pharmacology and molecular docking." Medicine 103, no. 1 (2024): e36852. http://dx.doi.org/10.1097/md.0000000000036852.

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Background: Kiwi root is a Chinese herb clinically used in the treatment of lung neoplasm; however, the multi-target mechanism of kiwi root in the treatment of non-small cell lung cancer (NSCLC) remains to be elucidated. Thus, this study aimed to investigate the molecular mechanisms of kiwi root in the treatment of NSCLC through network pharmacology and molecular docking techniques. Methods: The active components and targets of kiwi root were obtained from the TCMSP database, and NSCLC-related targets were obtained from the GeneCards, OMIM, and DrugBank databases. The intersection targets of N

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Winslett, Marianne, and Vanessa Braganholo. "Huanchen Zhang Speaks Out on Memory-Efficient Search Trees." ACM SIGMOD Record 50, no. 4 (2022): 47–49. http://dx.doi.org/10.1145/3516431.3516445.

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Welcome to ACM SIGMOD Record's series of interviews with distinguished members of the database community. I'm Marianne Winslett, and today I have here with me Huanchen Zhang, who is the 2021 winner of the ACM SIGMOD Jim Gray Dissertation Award for his thesis entitled Memory-Efficient Search Trees for Database Management Systems. After a postdoc at Snowflake, Huanchen is now an Assistant professor at Tsinghua University. His PhD is from Carnegie Mellon University, where he worked with David Andersen and Andy Pavlo. So, Huanchen, welcome!

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German, Benjamin D., Jeffrey Allen Borgia, Ankur D. Naqib, et al. "RNA pathway enrichment in serum-based mass spectroscopy prognostic analyses." Journal of Clinical Oncology 38, no. 15_suppl (2020): e15197-e15197. http://dx.doi.org/10.1200/jco.2020.38.15_suppl.e15197.

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e15197 Background: Veristrat(VS) good and poor labels were found to be prognostic in the front-line NSCLC setting with or without immune checkpoint inhibitors. Little is known about RNA expression data corresponding to these good and poor prognostic labels. Methods: Raw RNA seq expression data was obtained from TEMPUS XP RNA analysis. Sequences were filtered for allowing only genes that had an overall count of at least 20 across all samples. Samples were then processed through the EdgeR analysis in the R programming environment. Along with a Z-scored heatmap, PCA plot was also generated. Diffe

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Brown, Paul. "Knutson, Roslyn L., David McInnis, and Matthew Steggle, eds. The Lost Plays Database." Renaissance and Reformation 41, no. 4 (2018): 178. http://dx.doi.org/10.7202/1061920ar.

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Brown, Paul. "Knutson, Roslyn L., David McInnis, and Matthew Steggle, eds. The Lost Plays Database." Renaissance and Reformation 41, no. 4 (2019): 178–81. http://dx.doi.org/10.33137/rr.v41i4.32459.

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Liu, Huiping, Liuting Zeng, Kailin Yang, and Guomin Zhang. "A Network Pharmacology Approach to Explore the Pharmacological Mechanism of Xiaoyao Powder on Anovulatory Infertility." Evidence-Based Complementary and Alternative Medicine 2016 (2016): 1–13. http://dx.doi.org/10.1155/2016/2960372.

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Aim.To explore the pharmacological mechanism of Xiaoyao powder (XYP) on anovulatory infertility by a network pharmacology approach.Method.Collect XYP’s active compounds by traditional Chinese medicine (TCM) databases, and input them into PharmMapper to get their targets. Then note these targets by Kyoto Encyclopedia of Genes and Genomes (KEGG) and filter out targets that can be noted by human signal pathway. Get the information of modern pharmacology of active compounds and recipe’s traditional effects through databases. Acquire infertility targets by Therapeutic Target Database (TTD). Collect

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Roca-Cusachs, Marcos, Daniel Suárez, Víctor Osorio, et al. "Updated check-list and geographic database of new chorological data of true bugs (Insecta, Hemiptera, Heteroptera) from the Canary Islands." Arquivos Entomolóxicos 22 (May 23, 2020): 169–218. https://doi.org/10.5281/zenodo.12810539.

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Roca-Cusachs, Marcos, Suárez, Daniel, Osorio, Víctor, García-Becerra, Rafael, García-Pérez, Javier, Hernández-Teixidor, David, Pérez-Delgado, Antonio José, Pérez-Valcárcel, Javier, París, Mercedes, Oromí, Pedro, Goula, Marta (2020): Updated check-list and geographic database of new chorological data of true bugs (Insecta, Hemiptera, Heteroptera) from the Canary Islands. Arquivos Entomolóxicos 22: 169-218, DOI: 10.5281/zenodo.12810539

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Dedhia, Mehek, Kenneth Kohetuk, Wim E. Crusio, and Anna Delprato. "Introducing high school students to the Gene Ontology classification system." F1000Research 8 (April 15, 2019): 241. http://dx.doi.org/10.12688/f1000research.18061.2.

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We present a tutorial that introduces high school students to the Gene Ontology classification system which is widely used in genomics and systems biology studies to characterize large sets of genes based on functional and structural information. This classification system is a valuable and standardized method used to identify genes that act in similar processes and pathways and also provides insight into the overall architecture and distribution of genes and gene families associated with a particular tissue or disease. By means of this tutorial, students learn how the classification system wo

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Dedhia, Mehek, Kenneth Kohetuk, Wim E. Crusio, and Anna Delprato. "Introducing high school students to the Gene Ontology classification system." F1000Research 8 (May 24, 2019): 241. http://dx.doi.org/10.12688/f1000research.18061.3.

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We present a tutorial that introduces high school students to the Gene Ontology classification system which is widely used in genomics and systems biology studies to characterize large sets of genes based on functional and structural information. This classification system is a valuable and standardized method used to identify genes that act in similar processes and pathways and also provides insight into the overall architecture and distribution of genes and gene families associated with a particular tissue or disease. By means of this tutorial, students learn how the classification system wo

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Dedhia, Mehek, Kenneth Kohetuk, Wim E. Crusio, and Anna Delprato. "Introducing high school students to the Gene Ontology classification system." F1000Research 8 (August 6, 2019): 241. http://dx.doi.org/10.12688/f1000research.18061.4.

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We present a tutorial that introduces high school students to the Gene Ontology classification system which is widely used in genomics and systems biology studies to characterize large sets of genes based on functional and structural information. This classification system is a valuable and standardized method used to identify genes that act in similar processes and pathways and also provides insight into the overall architecture and distribution of genes and gene families associated with a particular tissue or disease. By means of this tutorial, students learn how the classification system wo

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19

Klimov, Kirill Yu. "Analysis of retinoblastoma-associated genes using bioinformatic methods." Digital Diagnostics 4, no. 1S (2023): 66–69. http://dx.doi.org/10.17816/dd430347.

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BACKGROUND: Retinoblastoma is a common neoplasia that affects the visual organ in young children. The mortality rate is approximately 15%. In 91% of cases, surgery with enucleation is required, which significantly reduces the patients quality of life. Early diagnosis of the disease may help to correct approaches to treatment of retinoblastoma, significantly increasing the chances of preserving vision. This is important since approximately 95% of retinoblastoma cases are diagnosed before the age of 5. Using bioinformatic methods, a comprehensive analysis of the patterns and connections between

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Chen, Riyu, Zeyi Guan, Xianxing Zhong, Wenzheng Zhang, and Ya Zhang. "Network Pharmacology Prediction: The Possible Mechanisms of Cinobufotalin against Osteosarcoma." Computational and Mathematical Methods in Medicine 2022 (January 13, 2022): 1–9. http://dx.doi.org/10.1155/2022/3197402.

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Objective. To explore the active compounds and targets of cinobufotalin (huachansu) compared with the osteosarcoma genes to obtain the potential therapeutic targets and pharmacological mechanisms of action of cinobufotalin on osteosarcoma through network pharmacology. Methods. The composition of cinobufotalin was searched by literature retrieval, and the target was selected from the CTD and TCMSP databases. The osteosarcoma genes, found from the GeneCards, OMIM, and other databases, were compared with the cinobufotalin targets to obtain potential therapeutic targets. The protein-protein intera

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McNiven, Ian J., Bruno David, and Josephine Flood. "Delamere 3: Further excavations at Yiwarlarlay (Lightning Brothers Site), Northern Territory." Australian Aboriginal Studies, no. 1 (January 1, 1992): 67——73. https://doi.org/10.5281/zenodo.6375948.

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As part of the research objectives of the Lightning Brothers Project, a series of excavations was undertaken at Yiwarlarlay, northwest Northern Territory (David et al 1990a; 1990b; 1991) (Map 1). Yiwarlarlay, or the Lightning Brothers Site, is an important Dreaming place for local Wardaman people, and consists of a spectacular sandstone outcrop exhibiting hundreds of paintings and engravings. The primary aims of the excavations were to provide chronological insights into paintings and engravings at the site, especially the large painted images of the Lightning Brothers - Yagjagbula and Jabirri

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Jing, Jing-jing, Hao Li, Ze-yang Wang, Heng Zhou, Li-ping Sun, and Yuan Yuan. "Aberrantly methylated-differentially expressed genes and pathways in Epstein–Barr virus-associated gastric cancer." Future Oncology 16, no. 6 (2020): 187–97. http://dx.doi.org/10.2217/fon-2019-0649.

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Aim: To identify the methylated-differentially expressed genes (MDEGs) that may serve as diagnostic markers and therapeutic targets in Epstein–Barr virus-associated gastric cancer (EBVaGC) and to explore the methylation-based pathways for elucidating biological mechanisms of EBVaGC. Materials & methods: Gene expression and methylation profiles were downloaded from GEO database. MDEGs were identified by GEO2R. Pathway enrichment analyses were conducted based on DAVID database. Hub genes were identified by Cytoscape, which were further verified by The Cancer Genome Atlas database. Results: A

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Zhong, Wan, Si-Yu Tao, Xiang Guo, et al. "Network pharmacology and molecular docking-based investigation on traditional Chinese medicine Astragalus membranaceus in oral ulcer treatment." Medicine 102, no. 34 (2023): e34744. http://dx.doi.org/10.1097/md.0000000000034744.

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To analyze the mechanism of Astragalus membranaceus (AM) in molecular level in the oral ulcer (OU) treatment with reference to network pharmacology. Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform database was used in screening the AM active components and AM action targets; GeneCards database was used to screen OU targets; the common target were screened by Venny online tool; Cytoscape software was applied to construct the target gene regulation map of AM active components; STRING database was used to construct the protein–protein interaction network and the k

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Zeng, Lu, Xiude Fan, Xiaoyun Wang, et al. "Bioinformatics Analysis based on Multiple Databases Identifies Hub Genes Associated with Hepatocellular Carcinoma." Current Genomics 20, no. 5 (2019): 349–61. http://dx.doi.org/10.2174/1389202920666191011092410.

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Background: Hepatocellular carcinoma (HCC) is the most common liver cancer and the mechanisms of hepatocarcinogenesis remain elusive. Objective: This study aims to mine hub genes associated with HCC using multiple databases. Methods: Data sets GSE45267, GSE60502, GSE74656 were downloaded from GEO database. Differentially expressed genes (DEGs) between HCC and control in each set were identified by limma software. The GO term and KEGG pathway enrichment of the DEGs aggregated in the datasets (aggregated DEGs) were analyzed using DAVID and KOBAS 3.0 databases. Protein-protein interaction (PPI) n

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Andrade, Preema K., Manjunatha Hanumanthappa, Vijayalakshmi Venkataramanaiah та Nayana Prakash. "Protein Interaction Network Analysis of β-catenin to Map its Crucial Interacting Genes using Systems Biology Approach". International Journal of Pharmaceutical Sciences and Drug Research 15, № 02 (2023): 176–88. http://dx.doi.org/10.25004/ijpsdr.2023.150209.

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β-catenin (CTNNB1), a scaffold protein, plays a vital role in embryonic development, adult tissue homeostasis, neurodegenerative diseases, bone diseases, chronic obstructive pulmonary diseases, wound healing, and pigment disorders. β-catenin is the crucial component in the Wnt-signaling pathway. β-catenin levels in the cytosol balance the Wnt-signaling pathway. The activated Wnt-signaling pathway allows the accumulation of β-catenin in the nucleus and further act as a promoter to initiate transcription of several oncogenes responsible for carcinogenesis. In the present study, we have used a sy

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Qiu, Mingyang, Jianqing Zhang, Wenlong Wei, et al. "Integrated UPLC/Q-TOF-MS/MS Analysis and Network Pharmacology to Reveal the Neuroprotective Mechanisms and Potential Pharmacological Ingredients of Aurantii Fructus Immaturus and Aurantii Fructus." Pharmaceuticals 17, no. 2 (2024): 239. http://dx.doi.org/10.3390/ph17020239.

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Aurantii Fructus (AF) and Aurantii Fructus Immaturus (AFI) have been used for thousands of years as traditional Chinese medicine (TCM) with sedative effects. Modern studies have shown that Citrus plants also have protective effects on the nervous system. However, the effective substances and mechanisms of action in Citrus TCMs still remain unclear. In order to explore the pharmacodynamic profiles of identified substances and the action mechanism of these herbs, a comprehensive approach combining ultra-high-performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC

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Meng, Fuxue, Xiaomai Tao, Longkuan Li, and Xin Yang. "Network Pharmacology-Based Study of Active Ingredients and Mechanisms of Compound Xuanju for Rheumatoid Arthritis." Journal of Current Medical Research and Opinion 3, no. 10 (2020): 712–23. http://dx.doi.org/10.15520/jcmro.v3i10.336.

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Objective: Compound Xuanju has good effects in treating rheumatoid arthritis (RA), but its composition is complex, and its active ingredients and mechanism have not been fully defined. In this study, the active ingredients and mechanism of compound Xuanju for the treatment of RA were explored through network pharmacological methods. Methods: TCMSP and TCMID, Pubmed, CNKI, Wanfang, and VIP databases were used to screen, select active pharmaceutical ingredients and targets; Drugbank disease target screening database, GeneCards database, Therapeutic The Target Database (TTD) database and DisGeNET

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Yang, Wan-Xia, Yun-Yan Pan, and Chong-Ge You. "CDK1, CCNB1, CDC20, BUB1, MAD2L1, MCM3, BUB1B, MCM2, and RFC4 May Be Potential Therapeutic Targets for Hepatocellular Carcinoma Using Integrated Bioinformatic Analysis." BioMed Research International 2019 (October 13, 2019): 1–16. http://dx.doi.org/10.1155/2019/1245072.

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Hepatocellular carcinoma (HCC) is a malignant tumor with high mortality. The abnormal expression of genes is significantly related to the occurrence of HCC. The aim of this study was to explore the differentially expressed genes (DEGs) of HCC and to provide bioinformatics basis for the occurrence, prevention and treatment of HCC. The DEGs of HCC and normal tissues in GSE102079, GSE121248, GSE84402 and GSE60502 were obtained using R language. The GO function analysis and KEGG pathway enrichment analysis of DEGs were carried out using the DAVID database. Then, the protein–protein interaction (PP

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Tian, Sha, Yinmei Guo, Jiajun Fu, Zijing Li, Jing Li, and Xuefei Tian. "Prognostic Value of Immunotyping Combined with Targeted Therapy in Patients with Non-Small-Cell Lung Cancer and Establishment of Nomogram Model." Computational and Mathematical Methods in Medicine 2022 (May 14, 2022): 1–9. http://dx.doi.org/10.1155/2022/3049619.

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Objective. Bioinformatics methods were used to analyze non-small-cell lung cancer gene chip data, screen differentially expressed genes (DEGs), explore biomarkers related to NSCLC prognosis, provide new targets for the treatment of NSCLC, and build immunotyping and line-map model. Methods. NSCLC-related gene chip data were downloaded from the GEO database, and the common DEGs of the two datasets were screened by using the GEO2R tool and FunRich 3.1.3 software. DAVID database was used for GO analysis and KEGG analysis of DEGs, and protein-protein interaction (PPI) network was constructed by STR

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Wang, Jinji, Ming Yang, Yuna Han, et al. "Research on the anti hyperlipidemia effect and signaling pathway of Polygonum multiflorum based on network pharmacology." Molecular & Cellular Biomechanics 22, no. 5 (2025): 1636. https://doi.org/10.62617/mcb1636.

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Objective: To investigate the mechanism and signaling pathway of Polygonum multiflorum in combating hyperlipidemia based on network pharmacology. Method: Search traditional Chinese medicine databases and literature to screen and integrate the active ingredients and target proteins of Polygonum multiflorum. Retrieve and obtain the active ingredients and targets of Polygonum multiflorum from the TCMSP database and DrugBank database. Construct a compound target network of Polygonum multiflorum and its corresponding protein-protein interaction (PPI) network in Cytoscape software, and perform gene

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Li, Wenwen, Guowei Zhang, Zhenfeng Zhao, Yaoyao Zuo, Zhenhai Sun, and Shouqiang Chen. "Exploring the mechanism of Erchen decoction in the treatment of atherosclerosis based on network pharmacology and molecular docking." Medicine 102, no. 46 (2023): e35248. http://dx.doi.org/10.1097/md.0000000000035248.

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Background: Atherosclerosis (AS) is the cause of most cardiovascular diseases and imposes a huge economic burden on society. Erchen decoction (ECD) is an effective formula for treating AS, but its therapeutic mechanism remains unclear. This study will explore the mechanism of ECD mechanism for treating AS using network pharmacology and molecular docking. Methods: We searched ECD chemical composition information and related targets via Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and SwissTargetPrediction databases, and gene names correction was performed usi

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Wang, Yan, Shengtao Shang, Kun Yu, Hongbin Sun, Wenduan Ma, and Wei Zhao. "miR-224, miR-147b and miR-31 associated with lymph node metastasis and prognosis for lung adenocarcinoma by regulating PRPF4B, WDR82 or NR3C2." PeerJ 8 (November 24, 2020): e9704. http://dx.doi.org/10.7717/peerj.9704.

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Background The present study is to screen lymph node metastasis-related microRNAs (miRNAs) in lung adenocarcinoma (LUAD) and uncover their underlying mechanisms. Methods The miRNA microarray dataset was collected from the Gene Expression Omnibus database under accession number GSE64859. The differentially expressed miRNAs (DEMs) were identified using a t-test. Target genes of DEMs were predicted through the miRWalk2.0 database. The function of these target genes was annotated with the clusterProfiler and the Database for Annotation, Visualization and Integrated Discovery (DAVID) tools. Protein

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Han, Jie, Guowu Ren, Zhiwei Xu, et al. "Exploring the relationship between systemic lupus erythematosus and osteoporosis based on bioinformatics." Lupus 31, no. 2 (2022): 163–77. http://dx.doi.org/10.1177/09612033211073909.

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Objective This study aimed to explore the relationship between systemic lupus erythematosus (SLE) and osteoporosis (OP) based on bioinformatics. Methods The expression profiles of SLE and OP gene chips were searched through the GEO database, and the differentially expressed genes (DEGs) were screened out to obtain the intersection. Then, the Funrich software was used to predict the upstream miRNAs of the intersection genes, and the miRNA–mRNA relationship network was constructed. Afterward, the String database and Cytoscape software were used to construct the protein interaction network of the

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Chen, Ting, Liang Zhang, Xulong Huang, et al. "Exploring the Potential Pharmacologic Mechanism of Heterophyllin B in the Treatment of Esophageal Cancer by Network Pharmacology." E3S Web of Conferences 271 (2021): 03036. http://dx.doi.org/10.1051/e3sconf/202127103036.

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This study used the method of network pharmacology to preliminarily predict the mechanism of Heterophyllin B(HB) inhibiting Esophageal Cancer(EC). We found the HB targets in the TCMSP and PuChem databases, and searched all EC-related targets in the GeneCards database. Taken the intersection of HB and EC as potential targets for inhibiting EC, and used Cytoscape 3.7.1 software to perform topological analysis on potential targets to obtain core targets. Used the start Analysisi function in the DAVID database to analyzed the biological process of the core target, and visualized it with the the R

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Chen, Ting, Haiyu Chen, Liang Zhang, et al. "Analysis of Oxoglaucine in the Treatment of Breast Cancer Based on Network Pharmacology and Bioinformatics." E3S Web of Conferences 271 (2021): 03078. http://dx.doi.org/10.1051/e3sconf/202127103078.

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To explore the potential molecular mechanism of Oxoglaucine(OG) in the treatment of Breast Cancer(BC) based on network pharmacology and bioinformatics. TCMSP and SwissTargetPrediction databases search for OG Related targets, and GeneCards database finds all BC-related targets. Take the intersection of OG and BC as all potential targets that inhibit BC. All potential targets are topologically analyzed by Cytoscape 3.7.1 software, and finally the core target is obtained. The start analysisi function in the DAVID database performs bioinformatics analysis on all core targets, and further visualize

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Li, Ningshan, Nayang Shan, Lingeng Lu, and Zuoheng Wang. "tRFtarget: a database for transfer RNA-derived fragment targets." Nucleic Acids Research 49, no. D1 (2020): D254—D260. http://dx.doi.org/10.1093/nar/gkaa831.

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Abstract Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http://trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including l

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Ren, Guo-wu, Shuai-bo Wen, Jie Han, et al. "Network-Based Pharmacology and Bioinformatics Study on the Mechanism of Action of Gujiansan in the Treatment of Steroid-Induced Avascular Necrosis of the Femoral Head." BioMed Research International 2022 (July 23, 2022): 1–17. http://dx.doi.org/10.1155/2022/8080679.

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Objective. To investigate the main pharmacological basis and mechanism of action of Gujiansan in the treatment of steroid-induced avascular necrosis of the femoral head (SANFH). Methods. The active constituents and targets of Gujiansan were screened by using TCMSP and other databases, and relevant disease targets were obtained by analyzing the microarray of SANFH in the GEO database. The intersection of the two was taken to obtain the potential targets of Gujiansan for the treatment of SANFH, and key active constituents were screened with the “active constituent-target” network constructed by

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Cai, Aiyuan, Siting Xu, Meiping Shi, et al. "Utilizing network p harmacology to investigate the probable mechanism of Danshen chuanxiong drug pair in Kawasaki disease." Tropical Journal of Pharmaceutical Research 23, no. 12 (2025): 2001–15. https://doi.org/10.4314/tjpr.v23i12.5.

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Purpose: To investigate the primary components and effect of Danshen-Chuanxiong (DS-CX) in the treatment of Kawasaki disease. Methods: Active ingredients of DS-CX and targets of action were screened via the Traditional Chinese Medicine Systematic Pharmacology (TCMSP) and SwissTargetPrediction databases. Targets of Kawasaki disease were queried in OMIM, GeneCards, DRUGBANK, and Disgenet databases, and intersected with drug targets. Protein-protein interaction maps (PPIs) were constructed using STRING database and Cytoscape software, and core genes of Kawasaki disease were screened. Pathway enri

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Wang, Chen, Ao-lei Liu, He-zhen Wu, and Yan-fang Yang. "Prediction the Molecular Mechanism of Shengmai Injection in Acute Treatment of COVID-19 Based on Network Pharmacology." Natural Product Communications 17, no. 2 (2022): 1934578X2210750. http://dx.doi.org/10.1177/1934578x221075075.

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Objective: To predict the mechanism of Shengmai Injection (SMI) in the acute treatment of COVID-19 by network pharmacology and molecular docking. Methods: Search the compounds in the Traditional Chinese Medicine Systems Pharmacology (TCMSP), and screen them by Drug-like properties (DL) and Oral bioavailability (OB); Using PharmMapper database and GeneCards database to collect compounds targets and COVID-19 targets, and using UniProt database to standardize the names of target genes; Using DAVID database for KEGG pathway annotation and GO bioinformatics analysis; Using Cytoscape 3.8.2 software

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Viswanathan, Sittarthan. "Insights from molecular network analysis to docking of sterubin with potential targets." Bioinformation 19, no. 12 (2023): 1184–92. http://dx.doi.org/10.6026/973206300191184.

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The use of a flavonoid compound sterubin in drug discovery is gaining momentum. Hence, it is of interest to document the molecular network analysis to docking of sterubin with potential targets to glean insights. We identified 32 target genes and (or) gene products for sterubin using DAVID tools for GO, KEGG pathway enrichment analyses and the STRING database. Further, molecular docking analysis data of sterubin with these targets is documented for further consideration in broad-spectrum drug discovery.

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Ding, Shanshan, Weihao Wang, Xujiao Song, and Hao Ma. "Based on Network Pharmacology and Molecular Docking to Explore the Underlying Mechanism of Huangqi Gegen Decoction for Treating Diabetic Nephropathy." Evidence-Based Complementary and Alternative Medicine 2021 (May 6, 2021): 1–14. http://dx.doi.org/10.1155/2021/9928282.

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Background. Huangqi Gegen decoction (HGD), a Chinese herb formula, has been widely used to treat diabetic nephropathy in China, while the pharmacological mechanisms are still unclear. Therefore, the present study aims to explore the underlying mechanism of HGD for treating diabetic nephropathy (DN). Materials and Methods. Traditional Chinese Medicine Systems Pharmacology Database (TCMSP), UniProt, and SwissTargetPrediction databases were used to search the active ingredients and potential targets of HGD. In addition, multiple disease-related databases were used to collect DN-related targets. C

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Luo, Xiang, Yunke Shi, Yiming Ma, et al. "Exploring the mechanism of ShenGui capsule in treating heart failure based on network pharmacology and molecular docking: A review." Medicine 103, no. 14 (2024): e37512. http://dx.doi.org/10.1097/md.0000000000037512.

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ShenGui capsule (SGC), as a herbal compound, has significant effects on the treatment of heart failure (HF), but its mechanism of action is unclear. In this study, we aimed to explore the potential pharmacological targets and mechanisms of SGC in the treatment of HF using network pharmacology and molecular docking approaches. Potential active ingredients of SGC were obtained from the traditional Chinese medicine systems pharmacology database and analysis platform database and screened by pharmacokinetic parameters. Target genes of HF were identified by comparing the toxicogenomics database, Ge

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Bi, De, Hua Jun Xiao, Cui Hong Zhou, and Jun Zhou. "Mining the Bioinformation of Differentially Expressed Genes in Obese Mice Treated with Chronic Intermittent Hypoxia Based on the Bioinformatics Methods." Applied Mechanics and Materials 195-196 (August 2012): 429–34. http://dx.doi.org/10.4028/www.scientific.net/amm.195-196.429.

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Objective: To analyze the differentially expressed genes expressed genes in obese mice that treated with chronic intermittent hypoxia (CIH) for getting better understanding of the molecular characteristics in the obese mice caused by CIH. Methods: Got the microarray hybridization data from the Gene Expression Omnibus (GEO) database. Identified the differentially expressed genes expressed genes in CIH obese mice and the patterns of their regulation using public bioinformatics software and database, such as BRB-Arraytools, Genecodis and DAVID, KEGG. Results and Conclusion: We found the Peroxisom

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Suliman, Yara, Frank Becker, and Klaus Wimmers. "Implication of transcriptome profiling of spermatozoa for stallion fertility." Reproduction, Fertility and Development 30, no. 8 (2018): 1087. http://dx.doi.org/10.1071/rd17188.

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Poor fertility of breeding stallions is a recognised problem in the equine industry. The aim of the present study was to detect molecular pathways using two groups of stallions that differed in pregnancy rates as well as in the proportion of normal and motile spermatozoa. RNA was isolated from spermatozoa of each stallion and microarray data were analysed to obtain a list of genes for which transcript abundance differed between the groups (P ≤0.05, fold change ≥1.2). In all, there were 437 differentially expressed (DE) genes between the two groups (P ≤ 0.05, fold change ≥1.2). Next, the DE gen

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Tong, Xiaojuan, Sumei Xu, and Dong Zhai. "Multiple Mechanisms of Shenqi Pill in Treating Nonalcoholic Fatty Liver Disease Based on Network Pharmacology and Molecular Docking." Evidence-Based Complementary and Alternative Medicine 2022 (June 26, 2022): 1–9. http://dx.doi.org/10.1155/2022/2384140.

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Background. Shenqi pill (SQP), a traditional Chinese prescription, has proven to be effective in treating nonalcoholic fatty liver disease (NAFLD). However, its bioactive ingredients and underlying mechanisms remain elusive. Aim. We aimed to predict the active compounds, potential targets, and molecular mechanisms of SQP anti-NAFLD by applying network pharmacology and molecular docking methods. Methods. Active ingredients and related targets of SQP were obtained from the TCMSP database. Potential targets of NAFLD were acquired from OMIM and GeneCards databases. The STRING database and Cytoscap

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Hu, Lili, Jue Wang, Na Wu, Xiaoge Zhao, and Donghui Cai. "Utilizing network pharmacology and experimental validation to investigate the underlying mechanism of phellodendrine on inflammation." PeerJ 10 (September 23, 2022): e13852. http://dx.doi.org/10.7717/peerj.13852.

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Background Phellodendrine, one of the characteristic and important active components of Cortex phellodendri, has been proven to show anti-inflammatory effects. However, the underlying mechanism of phellodendrine on inflammation remains largely unclear. Aim of the study In this study, network pharmacology and experimental validation were used to explore the underlying mechanism of phellodendrine on inflammation. Materials and Methods PubChem and SwissADME database were used to evaluate the drug-likeness and other characteristics of phellodendrine. The targets of phellodendrine for the treatment

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Gu, Xiaofei, Jiangang Ju, Qingqing Chen, Minjie Ge, and Huaqiong Huang. "Investigation into the potential mechanism and therapeutic targets of Cangzhu Erchen decoction for the treatment of chronic obstructive pulmonary disease based on bioinformatics and network pharmacology." Medicine 103, no. 33 (2024): e39338. http://dx.doi.org/10.1097/md.0000000000039338.

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This study aimed to elucidate the molecular mechanisms underlying the therapeutic effects of Cangzhu Erchen decoction (CZECD) in the treatment of chronic obstructive pulmonary disease (COPD) using microarray analysis, network pharmacology, and molecular docking. The active components and candidate targets of CZECD were obtained using the Traditional Chinese Medicine Systems Pharmacology Database and Analysis Platform and Swiss Target Prediction. COPD-related targets were collected from 5 databases. Access to drug-disease interface targets in the Venny platform. The Cytoscape program and the ST

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Li, Zhaoxing, Zhao Liu, Zhiting Shao, et al. "Identifying multiple collagen gene family members as potential gastric cancer biomarkers using integrated bioinformatics analysis." PeerJ 8 (May 25, 2020): e9123. http://dx.doi.org/10.7717/peerj.9123.

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Background Gastric cancer is one of the most common malignant cancers worldwide. Despite substantial developments in therapeutic strategies, the five-year survival rate remains low. Therefore, novel biomarkers and therapeutic targets involved in the progression of gastric tumors need to be identified. Methods We obtained the mRNA microarray datasets GSE65801, GSE54129 and GSE79973 from the Gene Expression Omnibus database to acquire differentially expressed genes (DEGs). We used the Database for Annotation, Visualization, and Integrated Discovery (DAVID) to analyze DEG pathways and functions,

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Jiang, Lan, Zhongquan Shi, and Yi Yang. "Network Pharmacology-Based Approach to Investigate the Molecular Targets of Rhubarb for Treating Cancer." Evidence-Based Complementary and Alternative Medicine 2021 (June 8, 2021): 1–8. http://dx.doi.org/10.1155/2021/9945633.

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Background. As a traditional Chinese medicine, rhubarb (also named Dahuang) is used to treat various diseases. Objective. To explore the possible antitumor mechanism of rhubarb by using network pharmacology and molecular docking in this study. Methods. Bioactive ingredients and related targets of rhubarb were obtained from the Traditional Chinese Medicine Systems Pharmacology (TCMSP) database. And the gene names corresponding to the proteins were found in the UniProt database. Then, the tumor-related targets were screened out from GeneCards and OMIM databases. Key antitumor targets of rhubarb

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Purwoko, Devit, Imam Civi Cartealy, Teuku Tajuddin, Diny Dinarti, and Sudarsono Sudarsono. "ANALISIS BIOINFORMATIKA BERBASIS WEB PADA SEKUEN GENOM PARSIAL SAGU (Metroxylon sagu Rottb.)." Jurnal Bioteknologi & Biosains Indonesia (JBBI) 5, no. 1 (2018): 98. http://dx.doi.org/10.29122/jbbi.v5i1.2878.

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WEB-based bioinformatic analysis on partial genome sequence of Sago (Metroxylon sagu Rottb.)ABSTRACTSago genome sequencing analysis is still very limited. This study is a preliminary study of sago sequence analysis obtained from NGS technology to understand and identify new genetic sequences that have homology to genes in the NCBI database. Sequences were analyzed using Blast2Go to determine the genetic function annotation, putative gene identification was performed on the Arabidopsis database using the BLASTx program with a 10-3 e-value limit on The Arabidopsis Information Resource (TAIR) (ht

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