miSEA: microRNA set enrichment analysis

Anders, 2010, Differential expression analysis for sequence count data, Genome Biol., 11, R106, 10.1186/gb-2010-11-10-r106 Bartel, 2004, MicroRNAs: genomics, biogenesis, mechanism, and function, Cell, 116, 281, 10.1016/S0092-8674(04)00045-5 Caldas, 2009, Probabilistic retrieval and visualization of biologically relevant microarray experiments, Bioinformatics, 25, i145, 10.1093/bioinformatics/btp215 Dean, 2005, Normal uniform mixture differential gene expression detection for cDNA microarrays, BMC Bioinf., 6, 173, 10.1186/1471-2105-6-173 Hall, 2009, The WEKA Data Mining Software: An Update, SIGKDD Explor., 11, 10, 10.1145/1656274.1656278 Hsu, 2014, miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions, Nucleic Acids Res., 42, D78, 10.1093/nar/gkt1266 Kolesnikov, 2014, ArrayExpress update - simplifying data submissions, Nucleic Acids Res. Kozomara, 2014, miRBase: annotating high confidence microRNAs using deep sequencing data, Nucleic Acids Res., 42, D68, 10.1093/nar/gkt1181 Lu, 2008, An analysis of human microRNA and disease associations, PLoS One, 3, e3420, 10.1371/journal.pone.0003420 Maragkakis, 2009, DIANA-microT web server: elucidating microRNA functions through target prediction, Nucleic Acids Res., 37, W273, 10.1093/nar/gkp292 Lu, 2010, TAM: A method for enrichment and depletion analysis of a microRNA category in a list of microRNAs, BMC Bioinf., 11, 419, 10.1186/1471-2105-11-419 Nam, 2009, MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression, Nucleic Acids Res., 37, W356, 10.1093/nar/gkp294 Ogul, 2011, Data integration in functional analysis of microRNAs, Curr. Bioinf., 6, 462, 10.2174/157489311798072945 Pauli, 2011, Non-coding RNAs as regulators of embryogenesis, Nat. Rev. Genet., 12, 136, 10.1038/nrg2904 Sales, 2010, MAGIA, a web-based tool for miRNA and genes integrated analysis, Nucleic Acids Res., 38, W352, 10.1093/nar/gkq423 Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102 Uhlmann, 2012, Global microRNA level regulation of EGFR-driven cell-cycle protein network in breast cancer, Mol. Syst. Biol., 8, 569, 10.1038/msb.2011.100 Ulitsky, 2010, Towards computational prediction of microRNA function and activity, Nucleic Acids Res., 38, e160, 10.1093/nar/gkq570 Xiao, 2008, miRecords: an integrated resource for microRNA-target interactions, Nucleic Acids Res., 37, D105, 10.1093/nar/gkn851 Wang, 2009, TransmiR: a transcription factor-microRNA regulation database, Nucleic Acids Res., 38, D119, 10.1093/nar/gkp803 Wu, 2009, CORNA: testing gene lists for regulation by microRNAs, Bioinformatics, 25, 832, 10.1093/bioinformatics/btp059