Comparative study on gene set and pathway topology-based enrichment methods
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Title
Comparative study on gene set and pathway topology-based enrichment methods
Authors
Keywords
Gene set analysis, Pathway topology, Enrichment methods, Simulations, Accuracy, Sensitivity
Journal
BMC BIOINFORMATICS
Volume 16, Issue 1, Pages -
Publisher
Springer Nature
Online
2015-10-23
DOI
10.1186/s12859-015-0751-5
References
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- (2013) H. Maciejewski BRIEFINGS IN BIOINFORMATICS
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- (2011) Zhongyu Liu et al. COMPARATIVE AND FUNCTIONAL GENOMICS
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- (2011) M. Affer et al. Journal of Oncology
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- (2010) B. Zheng et al. Science Translational Medicine
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- Comparative study of gene set enrichment methods
- (2009) Luca Abatangelo et al. BMC BIOINFORMATICS
- FKBP51 Affects Cancer Cell Response to Chemotherapy by Negatively Regulating Akt
- (2009) Huadong Pei et al. CANCER CELL
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- (2009) Yi Wang et al. NATURE MEDICINE
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- Identification of genes with abnormal expression changes in acute myeloid leukemia
- (2007) Derek L. Stirewalt et al. GENES CHROMOSOMES & CANCER
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