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For: Lopez F, Textoris J, Bergon A, Didier G, Remy E, Granjeaud S, Imbert J, Nguyen C, Puthier D. TranscriptomeBrowser: a powerful and flexible toolbox to explore productively the transcriptional landscape of the Gene Expression Omnibus database. PLoS One 2008;3:e4001. [PMID: 19104654 PMCID: PMC2602602 DOI: 10.1371/journal.pone.0004001] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2008] [Accepted: 11/25/2008] [Indexed: 11/18/2022]  Open
Number Cited by Other Article(s)
1
Bavais J, Chevallier J, Spinelli L, van de Pavert S, Puthier D. SciGeneX: enhancing transcriptional analysis through gene module detection in single-cell and spatial transcriptomics data. NAR Genom Bioinform 2025;7:lqaf043. [PMID: 40248490 PMCID: PMC12004220 DOI: 10.1093/nargab/lqaf043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2024] [Revised: 03/19/2025] [Accepted: 04/09/2025] [Indexed: 04/19/2025]  Open
2
Dawood M, Hamdoun S, Efferth T. Multifactorial Modes of Action of Arsenic Trioxide in Cancer Cells as Analyzed by Classical and Network Pharmacology. Front Pharmacol 2018;9:143. [PMID: 29535630 PMCID: PMC5835320 DOI: 10.3389/fphar.2018.00143] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 02/09/2018] [Indexed: 12/13/2022]  Open
3
Donaires FS, Godoy PRDV, Leandro GS, Puthier D, Sakamoto-Hojo ET. E2F transcription factors associated with up-regulated genes in glioblastoma. Cancer Biomark 2017;18:199-208. [PMID: 27983535 DOI: 10.3233/cbm-161628] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
4
Bergon A, Belzeaux R, Comte M, Pelletier F, Hervé M, Gardiner EJ, Beveridge NJ, Liu B, Carr V, Scott RJ, Kelly B, Cairns MJ, Kumarasinghe N, Schall U, Blin O, Boucraut J, Tooney PA, Fakra E, Ibrahim EC. CX3CR1 is dysregulated in blood and brain from schizophrenia patients. Schizophr Res 2015;168:434-43. [PMID: 26285829 DOI: 10.1016/j.schres.2015.08.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/25/2015] [Revised: 08/05/2015] [Accepted: 08/06/2015] [Indexed: 12/31/2022]
5
Malaney P, Pathak RR, Xue B, Uversky VN, Davé V. Intrinsic disorder in PTEN and its interactome confers structural plasticity and functional versatility. Sci Rep 2014;3:2035. [PMID: 23783762 PMCID: PMC3687229 DOI: 10.1038/srep02035] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022]  Open
6
Evangelista AF, Collares CVA, Xavier DJ, Macedo C, Manoel-Caetano FS, Rassi DM, Foss-Freitas MC, Foss MC, Sakamoto-Hojo ET, Nguyen C, Puthier D, Passos GA, Donadi EA. Integrative analysis of the transcriptome profiles observed in type 1, type 2 and gestational diabetes mellitus reveals the role of inflammation. BMC Med Genomics 2014;7:28. [PMID: 24885568 PMCID: PMC4066312 DOI: 10.1186/1755-8794-7-28] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2013] [Accepted: 03/27/2014] [Indexed: 01/12/2023]  Open
7
Fahrenbach JP, Andrade J, McNally EM. The CO-Regulation Database (CORD): a tool to identify coordinately expressed genes. PLoS One 2014;9:e90408. [PMID: 24599084 PMCID: PMC3944024 DOI: 10.1371/journal.pone.0090408] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2013] [Accepted: 02/01/2014] [Indexed: 02/03/2023]  Open
8
Santra T, Kolch W, Kholodenko BN. Navigating the multilayered organization of eukaryotic signaling: a new trend in data integration. PLoS Comput Biol 2014;10:e1003385. [PMID: 24550716 PMCID: PMC3923657 DOI: 10.1371/journal.pcbi.1003385] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]  Open
9
Wrangle J, Wang W, Koch A, Easwaran H, Mohammad HP, Vendetti F, VanCriekinge W, DeMeyer T, Du Z, Parsana P, Rodgers K, Yen RW, Zahnow CA, Taube JM, Brahmer JR, Tykodi SS, Easton K, Carvajal RD, Jones PA, Laird PW, Weisenberger DJ, Tsai S, Juergens RA, Topalian SL, Rudin CM, Brock MV, Pardoll D, Baylin SB. Alterations of immune response of Non-Small Cell Lung Cancer with Azacytidine. Oncotarget 2013;4:2067-79. [PMID: 24162015 PMCID: PMC3875770 DOI: 10.18632/oncotarget.1542] [Citation(s) in RCA: 304] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2013] [Accepted: 10/25/2013] [Indexed: 12/14/2022]  Open
10
Saadoun D, Terrier B, Bannock J, Vazquez T, Massad C, Kang I, Joly F, Rosenzwajg M, Sene D, Benech P, Musset L, Klatzmann D, Meffre E, Cacoub P. Expansion of autoreactive unresponsive CD21-/low B cells in Sjögren's syndrome-associated lymphoproliferation. ACTA ACUST UNITED AC 2013;65:1085-96. [PMID: 23279883 DOI: 10.1002/art.37828] [Citation(s) in RCA: 182] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2012] [Accepted: 12/07/2012] [Indexed: 11/07/2022]
11
Lepoivre C, Bergon A, Lopez F, Perumal NB, Nguyen C, Imbert J, Puthier D. TranscriptomeBrowser 3.0: introducing a new compendium of molecular interactions and a new visualization tool for the study of gene regulatory networks. BMC Bioinformatics 2012;13:19. [PMID: 22292669 PMCID: PMC3395838 DOI: 10.1186/1471-2105-13-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2011] [Accepted: 01/31/2012] [Indexed: 01/04/2023]  Open
12
Tseng GC, Ghosh D, Feingold E. Comprehensive literature review and statistical considerations for microarray meta-analysis. Nucleic Acids Res 2012;40:3785-99. [PMID: 22262733 PMCID: PMC3351145 DOI: 10.1093/nar/gkr1265] [Citation(s) in RCA: 285] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]  Open
13
van Dongen S, Abreu-Goodger C. Using MCL to extract clusters from networks. Methods Mol Biol 2012;804:281-95. [PMID: 22144159 DOI: 10.1007/978-1-61779-361-5_15] [Citation(s) in RCA: 266] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
14
Terrier B, Joly F, Vazquez T, Benech P, Rosenzwajg M, Carpentier W, Garrido M, Ghillani-Dalbin P, Klatzmann D, Cacoub P, Saadoun D. Expansion of Functionally Anergic CD21−/lowMarginal Zone-like B Cell Clones in Hepatitis C Virus Infection-Related Autoimmunity. THE JOURNAL OF IMMUNOLOGY 2011;187:6550-63. [DOI: 10.4049/jimmunol.1102022] [Citation(s) in RCA: 75] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
15
Baron D, Magot A, Ramstein G, Steenman M, Fayet G, Chevalier C, Jourdon P, Houlgatte R, Savagner F, Pereon Y. Immune response and mitochondrial metabolism are commonly deregulated in DMD and aging skeletal muscle. PLoS One 2011;6:e26952. [PMID: 22096509 PMCID: PMC3212519 DOI: 10.1371/journal.pone.0026952] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2011] [Accepted: 10/06/2011] [Indexed: 01/12/2023]  Open
16
Barrett T, Troup DB, Wilhite SE, Ledoux P, Evangelista C, Kim IF, Tomashevsky M, Marshall KA, Phillippy KH, Sherman PM, Muertter RN, Holko M, Ayanbule O, Yefanov A, Soboleva A. NCBI GEO: archive for functional genomics data sets--10 years on. Nucleic Acids Res 2010;39:D1005-10. [PMID: 21097893 PMCID: PMC3013736 DOI: 10.1093/nar/gkq1184] [Citation(s) in RCA: 831] [Impact Index Per Article: 55.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]  Open
17
Sex-related differences in gene expression following Coxiella burnetii infection in mice: potential role of circadian rhythm. PLoS One 2010;5:e12190. [PMID: 20730052 PMCID: PMC2921390 DOI: 10.1371/journal.pone.0012190] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2010] [Accepted: 07/22/2010] [Indexed: 12/20/2022]  Open
18
Acharya KK, Chandrashekar DS, Chitturi N, Shah H, Malhotra V, Sreelakshmi KS, Deepti H, Bajpai A, Davuluri S, Bora P, Rao L. A novel tissue-specific meta-analysis approach for gene expression predictions, initiated with a mammalian gene expression testis database. BMC Genomics 2010;11:467. [PMID: 20699007 PMCID: PMC3091663 DOI: 10.1186/1471-2164-11-467] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2010] [Accepted: 08/11/2010] [Indexed: 01/31/2023]  Open
19
Protein Bioinformatics Infrastructure for the Integration and Analysis of Multiple High-Throughput "omics" Data. Adv Bioinformatics 2010:423589. [PMID: 20369061 PMCID: PMC2847380 DOI: 10.1155/2010/423589] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2009] [Accepted: 01/05/2010] [Indexed: 12/26/2022]  Open
20
Genomics Portals: integrative web-platform for mining genomics data. BMC Genomics 2010;11:27. [PMID: 20070909 PMCID: PMC2824719 DOI: 10.1186/1471-2164-11-27] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2009] [Accepted: 01/13/2010] [Indexed: 12/21/2022]  Open
21
Herrmann C, Bérard S, Tichit L. SimCT: a generic tool to visualize ontology-based relationships for biological objects. ACTA ACUST UNITED AC 2009;25:3197-8. [PMID: 19776214 PMCID: PMC2778334 DOI: 10.1093/bioinformatics/btp553] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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