Toward a gold standard for benchmarking gene set enrichment analysis.
作者： Martin Morgan , Ralf Zimmer , Levi Waldron , Ludwig Geistlinger , Gergely Csaba
DOI: 10.1093/BIB/BBZ158
关键词:
摘要: … For expression-based EA on the full expression matrix, we … ), we recommend ROAST or GSVA that both test a directional hypothesis (… The main strength of GSVA lies in its capabilities for …
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sci-hub.se 参考文章(77)
Gene Ontology Consortium, None, Gene Ontology Consortium: going forward Nucleic Acids Research. ,vol. 43, ,(2015) , 10.1093/NAR/GKU1179
Noa Rappaport, Michal Twik, Noam Nativ, Gil Stelzer, Iris Bahir, Tsippi Iny Stein, Marilyn Safran, Doron Lancet, MalaCards: A Comprehensive Automatically-Mined Database of Human Diseases. Current protocols in human genetics. ,vol. 47, ,(2014) , 10.1002/0471250953.BI0124S47
Michaela Bayerlová, Klaus Jung, Frank Kramer, Florian Klemm, Annalen Bleckmann, Tim Beißbarth, Comparative study on gene set and pathway topology-based enrichment methods BMC Bioinformatics. ,vol. 16, pp. 334- 334 ,(2015) , 10.1186/S12859-015-0751-5
Luca Abatangelo, Rosalia Maglietta, Angela Distaso, Annarita D'Addabbo, Teresa Creanza, Sayan Mukherjee, Nicola Ancona, Comparative study of gene set enrichment methods. BMC Bioinformatics. ,vol. 10, pp. 275- 275 ,(2009) , 10.1186/1471-2105-10-275
Huaiyu Mi, Anushya Muruganujan, John T Casagrande, Paul D Thomas, Large-scale gene function analysis with the PANTHER classification system Nature Protocols. ,vol. 8, pp. 1551- 1566 ,(2013) , 10.1038/NPROT.2013.092
Günter P. Wagner, Koryu Kin, Vincent J. Lynch, Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory in Biosciences. ,vol. 131, pp. 281- 285 ,(2012) , 10.1007/S12064-012-0162-3
L. Geistlinger, G. Csaba, S. Dirmeier, R. Kuffner, R. Zimmer, A comprehensive gene regulatory network for the diauxic shift in Saccharomyces cerevisiae Nucleic Acids Research. ,vol. 41, pp. 8452- 8463 ,(2013) , 10.1093/NAR/GKT631
Wolfgang Huber, Vincent J Carey, Robert Gentleman, Simon Anders, Marc Carlson, Benilton S Carvalho, Hector Corrada Bravo, Sean Davis, Laurent Gatto, Thomas Girke, Raphael Gottardo, Florian Hahne, Kasper D Hansen, Rafael A Irizarry, Michael Lawrence, Michael I Love, James MacDonald, Valerie Obenchain, Andrzej K Oleś, Hervé Pagès, Alejandro Reyes, Paul Shannon, Gordon K Smyth, Dan Tenenbaum, Levi Waldron, Martin Morgan, Orchestrating high-throughput genomic analysis with Bioconductor Nature Methods. ,vol. 12, pp. 115- 121 ,(2015) , 10.1038/NMETH.3252
B. Zhang, S. Kirov, J. Snoddy, WebGestalt: an integrated system for exploring gene sets in various biological contexts Nucleic Acids Research. ,vol. 33, pp. 741- 748 ,(2005) , 10.1093/NAR/GKI475
C. Backes, A. Keller, J. Kuentzer, B. Kneissl, N. Comtesse, Y. A. Elnakady, R. Muller, E. Meese, H.-P. Lenhof, GeneTrail--advanced gene set enrichment analysis Nucleic Acids Research. ,vol. 35, pp. W186- W192 ,(2007) , 10.1093/NAR/GKM323