Abstract
Most high-throughput methods which are used in molecular biology generate gene lists. Interpreting large gene lists can reveal mechanistic insights and generate useful testable hypotheses. The process can be cumbersome and challenging. Multiple commercial and open solution currently exist that can aid researchers in the functional annotation of gene lists. The process of gene set annotation includes dataset preparation, which is method specific, gene list annotation and analysis and interpretation of the significant associations that were found. In this chapter, we demonstrate how WebGestalt can be applied to gene lists generated from transcriptional profiling data.
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References
Huang DW, Sherman BT, Lempicki RA (2009) Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res 37(1):1–13 [cited 2012 Sep 9]
Käll L, Vitek O (2011) Computational mass spectrometry-based proteomics. PLoS Comput Biol 7(12):e1002277 [cited 2012 Sep 9]
Ji H (2010) Computational analysis of ChIP-seq data [Internet]. In: Ladunga I (ed). Computational biology of transcription factor binding. Humana Press, Totowa, NJ, pp 143–159. http://www.springerlink.com/content/t64851482l360075/abstract/. Accessed Sep 9 2012
Kiefer J, Yin HH, Que QQ, Mousses S (2009) High-throughput siRNA screening as a method of perturbation of biological systems and identification of targeted pathways coupled with compound screening [Internet]. In: Nikolsky Y, Bryant J (eds) Protein networks and pathway analysis. Humana Press, Totowa, NJ, pp 275–287. [cited 2012 Sep 9] Available from: http://www.springerlink.com/content/m710w44457184447/abstract/
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP (2005) Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A 102(43):15545–15550 [cited 2012 Sep 8]
Liberzon A, Subramanian A, Pinchback R, Thorvaldsdóttir H, Tamayo P, Mesirov JP (2011) Molecular signatures database (MSigDB) 3.0. Bioinformatics 27(12):1739–1740 [cited 2012 Sep 9]
Matys V (2006) TRANSFAC(R) and its module TRANSCompel(R): transcriptional gene regulation in eukaryotes. Nucleic Acids Res 34(90001):D108–D110 [cited 2012 Sep 9]
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25(1):25–29 [cited 2012 Sep 9]
Khatri P, Sirota M, Butte AJ (2012) Ten years of pathway analysis: current approaches and outstanding challenges. PLoS Comput Biol 8(2):e1002375 [cited 2012 Sep 8]
Zhang B, Kirov S, Snoddy J (2005) WebGestalt: an integrated system for exploring gene sets in various biological contexts. Nucleic Acids Res 33(Web Server):W741–W748 [cited 2012 Sep 11]
Ji R-R, Chasalow S, Wang L, Hamid O, Schmidt H, Cogswell J, Alaparthy S, Berman D, Jure-Kunkel M, Siemers N, Jackson J, Shahabi V (2012) An immune-active tumor microenvironment favors clinical response to ipilimumab. Cancer Immunol Immunother 61(7):1019–1031 [cited 2012 Sep 11]
Enright AJ, Van Dongen S, Ouzounis CA (2002) An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res 30(7):1575–1584 [cited 2012 Sep 30]
Draghici S (2011) Statistics and data analysis for microarrays using R and bioconductor, 2nd edn. CRC Press, Boca Raton, FL
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Kirov, S., Ji, R., Wang, J., Zhang, B. (2014). Functional Annotation of Differentially Regulated Gene Set Using WebGestalt: A Gene Set Predictive of Response to Ipilimumab in Tumor Biopsies. In: Ochs, M. (eds) Gene Function Analysis. Methods in Molecular Biology, vol 1101. Humana Press, Totowa, NJ. https://doi.org/10.1007/978-1-62703-721-1_3
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DOI: https://doi.org/10.1007/978-1-62703-721-1_3
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