CGPS: A machine learning-based approach integrating multiple gene set analysis tools for better prioritization of biologically relevant pathways
Tài liệu tham khảo
Akers, 2010, VE-cadherin and PECAM-1 enhance ALL migration across brain microvascular endothelial cell monolayers, Exp. Hematol., 38, 733, 10.1016/j.exphem.2010.05.001
Alhamdoosh, 2017, Combining multiple tools outperforms individual methods in gene set enrichment analyses, Bioinformatics, 33, 414, 10.1093/bioinformatics/btw623
Anguille, 2011, Interferon-α in acute myeloid leukemia: an old drug revisited, Leukemia, 25, 739, 10.1038/leu.2010.324
Atadja, 2009, Development of the pan-DAC inhibitor panobinostat (LBH589): successes and challenges, Cancer Lett., 280, 233, 10.1016/j.canlet.2009.02.019
Barry, 2005, Significance analysis of functional categories in gene expression studies: a structured permutation approach, Bioinforma. Oxf. Engl., 21, 1943, 10.1093/bioinformatics/bti260
Bayerlová, 2015, Comparative study on gene set and pathway topology-based enrichment methods, BMC Bioinformatics, 16, 334, 10.1186/s12859-015-0751-5
Bernhard, 2001, Inhibition of histone deacetylase activity enhances Fas receptor-mediated apoptosis in leukemic lymphoblasts, Cell Death Differ., 8, 1014, 10.1038/sj.cdd.4400914
Bolden, 2006, Anticancer activities of histone deacetylase inhibitors, Nat. Rev. Drug Discov., 5, 769, 10.1038/nrd2133
Buchwald, 2009, HDACi--targets beyond chromatin, Cancer Lett., 280, 160, 10.1016/j.canlet.2009.02.028
Chiaretti, 2004, Gene expression profile of adult T-cell acute lymphocytic leukemia identifies distinct subsets of patients with different response to therapy and survival, Blood, 103, 2771, 10.1182/blood-2003-09-3243
Chiron, 2008, Toll-like receptors: lessons to learn from normal and malignant human B cells, Blood, 112, 2205, 10.1182/blood-2008-02-140673
Croft, 2011, Reactome: a database of reactions, pathways and biological processes, Nucleic Acids Res., 39, D691, 10.1093/nar/gkq1018
Desouza, 2012, The actin cytoskeleton as a sensor and mediator of apoptosis, BioArchitecture, 2, 75, 10.4161/bioa.20975
Dong, 2016, LEGO: a novel method for gene set over-representation analysis by incorporating network-based gene weights, Sci. Rep., 6
Edgar, 2002, Gene Expression Omnibus: NCBI gene expression and hybridization array data repository, Nucleic Acids Res., 30, 207, 10.1093/nar/30.1.207
Efron, 2007, On testing the significance of sets of genes, Ann. Appl. Stat., 1, 107, 10.1214/07-AOAS101
Fang, 2012, MicroRNA-143 (miR-143) regulates cancer glycolysis via targeting hexokinase 2 gene, J. Biol. Chem., 287, 23227, 10.1074/jbc.M112.373084
Fang, 2012, A network-based gene-weighting approach for pathway analysis, Cell Res., 22, 565, 10.1038/cr.2011.149
Fogg, 2014, Class IIa histone deacetylases are conserved regulators of circadian function, J. Biol. Chem., 289, 34341, 10.1074/jbc.M114.606392
Fumarola, 2014, Targeting PI3K/AKT/mTOR pathway in non small cell lung cancer, Biochem. Pharmacol., 90, 197, 10.1016/j.bcp.2014.05.011
Gaarenstroom, 2014, TGF-β signaling to chromatin: how Smads regulate transcription during self-renewal and differentiation, Semin. Cell Dev. Biol., 32, 107, 10.1016/j.semcdb.2014.01.009
Geistlinger, 2016, Bioconductor's EnrichmentBrowser: seamless navigation through combined results of set- & network-based enrichment analysis, BMC Bioinformatics, 17, 45, 10.1186/s12859-016-0884-1
Glenisson, 2007, Histone deacetylase 4 is required for TGFβ1-induced myofibroblastic differentiation, Biochim. Biophys. Acta BBA - Mol. Cell Res., 1773, 1572, 10.1016/j.bbamcr.2007.05.016
Goeman, 2007, Analyzing gene expression data in terms of gene sets: methodological issues, Bioinforma. Oxf. Engl., 23, 980, 10.1093/bioinformatics/btm051
Goeman, 2004, A global test for groups of genes: testing association with a clinical outcome, Bioinforma. Oxf. Engl., 20, 93, 10.1093/bioinformatics/btg382
Gu, 2013, CePa: an R package for finding significant pathways weighted by multiple network centralities, Bioinforma. Oxf. Engl., 29, 658, 10.1093/bioinformatics/btt008
Gumy-Pause, 2004, ATM gene and lymphoid malignancies, Leukemia, 18, 238, 10.1038/sj.leu.2403221
Hänzelmann, 2013, GSVA: gene set variation analysis for microarray and RNA-Seq data, BMC Bioinformatics, 14, 7, 10.1186/1471-2105-14-7
Kanehisa, 2000, KEGG: kyoto encyclopedia of genes and genomes, Nucleic Acids Res., 28, 27, 10.1093/nar/28.1.27
Kanehisa, 2010, KEGG for representation and analysis of molecular networks involving diseases and drugs, Nucleic Acids Res., 38, D355, 10.1093/nar/gkp896
Khatri, 2012, Ten years of pathway analysis: current approaches and outstanding challenges, PLoS Comput. Biol., 8, 10.1371/journal.pcbi.1002375
Law, 2014, voom: precision weights unlock linear model analysis tools for RNA-seq read counts, Genome Biol., 15, R29, 10.1186/gb-2014-15-2-r29
Liu, 2013, Blocking the class I histone deacetylase ameliorates renal fibrosis and inhibits renal fibroblast activation via modulating TGF-beta and EGFR signaling, PLoS One, 8
Livrea, 1985, Acute changes in blood-CSF barrier permselectivity to serum proteins after intrathecal methotrexate and CNS irradiation, J. Neurol., 231, 336
Luciano, 2014, Kidney involvement in leukemia and lymphoma, Adv. Chron. Kidney Dis., 21, 27, 10.1053/j.ackd.2013.07.004
Luo, 2009, GAGE: generally applicable gene set enrichment for pathway analysis, BMC Bioinformatics, 10, 161, 10.1186/1471-2105-10-161
Mayerhofer, 2004, Identification of heme oxygenase-1 as a novel BCR/ABL-dependent survival factor in chronic myeloid leukemia, Cancer Res., 64, 3148, 10.1158/0008-5472.CAN-03-1200
Parkinson, 2007, ArrayExpress--a public database of microarray experiments and gene expression profiles, Nucleic Acids Res., 35, D747, 10.1093/nar/gkl995
Patel, 2009, A dyad of lymphoblastic lysosomal cysteine proteases degrades the antileukemic drug l-asparaginase, J. Clin. Invest., 119, 1964
Pitt, 2015, CXCL12-producing vascular endothelial niches control acute T cell leukemia maintenance, Cancer Cell, 27, 755, 10.1016/j.ccell.2015.05.002
Rahmatallah, 2016, Gene set analysis approaches for RNA-seq data: performance evaluation and application guideline, Briefings Bioinf., 17, 393, 10.1093/bib/bbv069
Ranganathan, 2014, Guidance cue Netrin-1 and the regulation of inflammation in acute and chronic kidney disease, Mediat. Inflamm., 2014, 10.1155/2014/525891
Rasheed, 2008, Histone deacetylase inhibitors in lymphoma and solid malignancies, Expert Rev. Anticancer Ther., 8, 413, 10.1586/14737140.8.3.413
Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616
Schaefer, 2009, PID: the pathway interaction database, Nucleic Acids Res., 37, D674, 10.1093/nar/gkn653
Siegel, 2003, Cytostatic and apoptotic actions of TGF-β in homeostasis and cancer, Nat. Rev. Cancer, 3, 807, 10.1038/nrc1208
Smyth, 2005, Limma: linear models for microarray data, 397
Staal, 2008, Signaling pathways involved in the development of T-cell acute lymphoblastic leukemia, Haematologica, 93, 493, 10.3324/haematol.12917
Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. U. S. A., 102, 15545, 10.1073/pnas.0506580102
Takahashi, 2017, Rituximab protects podocytes and exerts anti-proteinuric effects in rat adriamycin-induced nephropathy independent of B-lymphocytes, Nephrol. Carlton Vic., 22, 49, 10.1111/nep.12737
Tarca, 2013, A comparison of gene set analysis methods in terms of sensitivity, prioritization and specificity, PLoS One, 8, 10.1371/journal.pone.0079217
Tarca, 2012, Down-weighting overlapping genes improves gene set analysis, BMC Bioinformatics, 13, 136, 10.1186/1471-2105-13-136
The Cancer Genome Atlas Research Network, 2013, The cancer genome Atlas Pan-cancer analysis project, Nat. Genet., 45, 1113, 10.1038/ng.2764
Tomfohr, 2005, Pathway level analysis of gene expression using singular value decomposition, BMC Bioinformatics, 6, 225, 10.1186/1471-2105-6-225
Tripathi, 2012, Assessment method for a power analysis to identify differentially expressed pathways, PLoS One, 7, 10.1371/journal.pone.0037510
Van de Wetering, 2002, WNT signaling and lymphocyte development, Cell, 109, S13, 10.1016/S0092-8674(02)00709-2
Visani, 2000, Alpha-interferon improves survival and remission duration in P-190BCR-ABL positive adult acute lymphoblastic leukemia, Leukemia, 14, 22, 10.1038/sj.leu.2401641
Wahaib, 2016, Panobinostat: a histone deacetylase inhibitor for the treatment of relapsed or refractory multiple myeloma, Am. J. Health-Syst. Pharm. AJHP Off. J. Am. Soc. Health-Syst. Pharm., 73, 441, 10.2146/ajhp150487
Yetgin, 2004, Evaluation of kidney damage in patients with acute lymphoblastic leukemia in long-term follow-up: value of renal scan, Am. J. Hematol., 77, 132, 10.1002/ajh.20146
Zhang, 2009, KEGGgraph: a graph approach to KEGG PATHWAY in R and bioconductor, Bioinformatics, 25, 1470, 10.1093/bioinformatics/btp167
