Principle Angle Enrichment Analysis (PAEA): Dimensionally reduced multivariate gene set enrichment analysis tool

Proceedings - 2015 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2015

Volumn , Issue , 2015, Pages 256-262

  Clark, Neil R ^a,b,c   Szymkiewicz, Maciej ^d   Wang, Zichen ^a,b,c   Monteiro, Caroline D ^a,b,c   Jones, Matthew R ^a,b,c   Ma'ayan, Avi ^a,b,c  

^a MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^b Library of Integrated Network based Cellular Signatures (LINCS)   (Poland)

^c Mount Sinai Knowledge Management Center (KMC)   (Poland)

^d POLISH ACADEMY OF SCIENCES   (Poland)

Author keywords

dimensionality reduction; gene set analysis; multivariate; online enrichment analysis tool

Indexed keywords

BENCHMARKING; BIOINFORMATICS; GENE EXPRESSION; GENES; WEBSITES;

ANALYSIS TOOLS; BIOLOGICAL INTERPRETATION; DIFFERENTIAL GENE EXPRESSIONS; DIFFERENTIALLY EXPRESSED GENE; DIMENSIONALITY REDUCTION; GENE SET ENRICHMENT ANALYSIS; GEOMETRICAL APPROACHES; MULTIVARIATE;

MULTIVARIANT ANALYSIS;

EID: 84962436318     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBM.2015.7359689     Document Type: Conference Paper

References (21)

1. D. Nam and S.-Y. Kim. "Gene-set approach for expression pattern analysis, " Briefings in bioinformatics, vol. 9, no. 3, pp. 189-197, 2008.
2. D. W. Huang, B. T. Sherman, and R. A. Lempicki, "BioInformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, " Nucleic acids research, vol. 37, no. 1, pp. 1-13, 2009.
3. B. Efron and R. Tibshirani, "On testing the significance of sets of genes, " The annals of applied statistics, pp. 107-129, 2007.
4. I. Dinu, J. D. Potter, T. Mueller, Q. Liu, A. J. Adewale, G. S. Jhangri, G. Einecke, K. S. Famulski, P. Halloran, and Y. Yasui, "Gene-set analysis and reduction, " Briefings in bioinformatics, vol. 10, no. 1, pp. 24-34, 2009.
5. M. Ackermann and K. Strimmer, "A general modular framework for gene set enrichment analysis, " BMC bioinformatics, vol. 10, no. 1, p. 47, 2009.
6. N. R. Clark, K. S. Hu, A. S. Feldmann, Y. Kou, E. Y. Chen, Q. Duan, and A. Ma'ayan, "The characteristic direction: a geometrical approach to identify differentially expressed genes, " BMC bioinformatics, vol. 15, no. 1, p. 79, 2014.
7. J.-H. Hung, T.-H. Yang, Z. Hu, Z. Weng, and C. DeLisi, "Gene set enrichment analysis: performance evaluation and usage guidelines, " Briefings in bioinformatics, p. bbr049, 2011.
8. A. Subramanian, P. Tamayo, V. K. Mootha, S. Mukherjee, B. L. Ebert, M. A. Gillette, A. Paulovich, S. L. Pomeroy, T. R. Golub, E. S. Lander et al., "Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, " Proceedings of the National Academy of Sciences of the United States of America, vol. 102, no. 43, pp. 15545-15550, 2005.
9. S. W. Kong, W. T. Pu, and P. J. Park, "A multivariate approach for integrating genome-wide expression data and biological knowledge, " BioInformatics, vol. 22, no. 19, pp. 2373-2380, 2006.
10. M. Hummel, R. Meister, and U. Mansmann, " Globalancova: exploration and assessment of gene group effects;' BioInformatics, vol. 24, no. 1, pp. 78-85, 2008.
11. J. J. Goeman, S. A. Van De Geer, F. De Kort, and H. C. Van Houwelingen, "A global test for groups of genes: testing association with a clinical outcome, " BioInformatics, vol. 20, no. 1, pp. 93-99, 2004.
12. A. Lachmann, H. Xu, J. Krishnan, S. I. Berger, A. R. Mazloom, and A. Ma'ayan, "Chea: transcription factor regulation inferred from integrating genome-wide chip-x experiments, " BioInformatics, vol. 26, no. 19, pp. 2438-2444, 2010.
13. T. Lu, Y. Pan, S .-Y. Kao, C. Li, I. Kohane, J. Chan, and B. A. Yankner, "Gene regulation and DNA damage in the ageing human brain, " Nature, vol. 429, no. 6994, pp. 883-891, 2004.
14. W. W. Pang, E. A. Price, D. Sahoo, I. Beerman, W. J. Maloney, D. J. Rossi, S. L. Schrier, and I. L. Weissman, "Human bone marrow hematopoietic stem cells are increased in frequency and myeloid-biased with age, " Proceedings of the National Academy of Sciences, vol. \08, no. 50, pp. 20012-20017, 2011.
15. S. Welle, A. I. Brooks, J. M. Delehanty, N. Needler, K. Bhatt, B. Shah, and C. A. Thornton, "Skeletal muscle gene expression profiles in 20-29 year old and 65-71 year old women, " Experimental gerontology, vol. 39, no. 3, pp. 369-377, 2004.
16. S. Welle, A. J. Brooks, and C. A. Thornton, "Computational method for reducing variance with affymetrix microarrays, " BMC bioinformatics, vol. 3, no. 1, p. 23, 2002.
17. Z. Zhang, S. Schwartz, L. Wagner, and W. Miller, "A greedy algorithm for aligning DNA sequences, " Journal of Computational biology, vol. 7, no. 1-2, pp. 203-214, 2000.
18. C. Beeley, Web Application Development with R Using Shiny. Packt Publishing Ltd, 2013.
19. M. Bostock, V. Ogievetsky, and J. Heer, "D3 data-driven documents, " Visualization and Computer Graphics, IEEE Transactions on, vol. 17, no. 12, pp. 2301-2309, 2011.
20. G. W. Gundersen, M. R. Jones, A. D. Rouillard, Y. Kou, C. D. Monteiro, A. S. Feldmann, K. S. Hu, and A. Ma'ayan, "Ge02enrichr: browser extension and server app to extract gene sets from geo and analyze them for biological functions, " BioInformatics, 2015.
21. E. Y. Chen, C. M. Tan, Y. Kou, Q. Duan, Z. Wang, G. V. Meirelles, N. R. Clark, and A. Ma'ayan, "Enrichr: interactive and collaborative htm15 gene list enrichment analysis tool;' BMC bioinformatics, vol. 14, no. 1, p. 128, 2013.