Abstract
Gene-set enrichment analysis finds functionally coherent gene-sets, such as pathways, that are statistically overrepresented in a given gene list. Ideally, the number of resulting sets is smaller than the number of genes in the list, thus simplifying interpretation. However, the increasing number and redundancy of gene-sets used by many current enrichment analysis resources work against this ideal. “Enrichment Map” is a Cytoscape plug-in that helps overcome gene-set redundancy and aids in the interpretation of enrichment results. Gene-sets are organized in a network, where each set is a node and links represent gene overlap between sets. Automated network layout groups related gene-sets into network clusters, enabling the user to quickly identify the major enriched functional themes and more easily interpret enrichment results.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Allison, D. B., Cui, X., Page, G. P., and Sabripour, M. (2006) Microarray data analysis: from disarray to consolidation and consensus., Nature reviews. Genetics 7, 55–65.
Huang da, W., Sherman, B. T., Tan, Q., Collins, J. R., Alvord, W. G., Roayaei, J., Stephens, R., Baseler, M. W., Lane, H. C., and Lempicki, R. A. (2007) The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists, Genome Biol 8, R183.
Huang da, W., Sherman, B. T., and Lempicki, R. A. (2009) Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc 4, 44–57.
Subramanian, A., Tamayo, P., Mootha, V. K., Mukherjee, S., Ebert, B. L., Gillette, M. A., Paulovich, A., Pomeroy, S. L., Golub, T. R., Lander, E. S., and Mesirov, J. P. (2005) 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 102, 15545–15550.
Isserlin, R., Merico, D., Alikhani-Koupaei, R., Gramolini, A., Bader, G. D., and Emili, A. (2010) Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps. Proteomics 1316–1327.
Shannon, P., Markiel, A., Ozier, O., Baliga, N. S., Wang, J. T., Ramage, D., Amin, N., Schwikowski, B., and Ideker, T. (2003) Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res 13, 2498–2504.
Cline, M. S., Smoot, M., Cerami, E., Kuchinsky, A., Landys, N., Workman, C., Christmas, R., Avila-Campilo, I., Creech, M., Gross, B., Hanspers, K., Isserlin, R., Kelley, R., Killcoyne, S., Lotia, S., Maere, S., Morris, J., Ono, K., Pavlovic, V., Pico, A. R., Vailaya, A., Wang, P.-L., Adler, A., Conklin, B. R., Hood, L., Kuiper, M., Sander, C., Schmulevich, I., Schwikowski, B., Warner, G. J., Ideker, T., and Bader, G. D. (2007) Integration of biological networks and gene expression data using Cytoscape., Nature protocols 2, 2366–2382.
Lin, C.-Y., Vega, V. B., Thomsen, J. S., Zhang, T., Kong, S. L., Xie, M., Chiu, K. P., Lipovich, L., Barnett, D. H., Stossi, F., Yeo, A., George, J., Kuznetsov, V. A., Lee, Y. K., Charn, T. H., Palanisamy, N., Miller, L. D., Cheung, E., Katzenellenbogen, B. S., Ruan, Y., Bourque, G., Wei, C.-L., and Liu, E. T. (2007) Whole-genome cartography of estrogen receptor alpha binding sites., PLoS genetics 3, e87.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2011 Springer Science+Business Media, LLC
About this protocol
Cite this protocol
Merico, D., Isserlin, R., Bader, G.D. (2011). Visualizing Gene-Set Enrichment Results Using the Cytoscape Plug-in Enrichment Map. In: Cagney, G., Emili, A. (eds) Network Biology. Methods in Molecular Biology, vol 781. Humana Press. https://doi.org/10.1007/978-1-61779-276-2_12
Download citation
DOI: https://doi.org/10.1007/978-1-61779-276-2_12
Published:
Publisher Name: Humana Press
Print ISBN: 978-1-61779-275-5
Online ISBN: 978-1-61779-276-2
eBook Packages: Springer Protocols