E-learning in analysis of genomic and proteomic data 2. Data analysis 2.2. Analysis of high-density genomic data 2.2.1. DNA microarrays Pathway Analysis References

Alexa, A., Rahnenführer, J., and Lengauer, T. (2006). Improved scoring of functional groups from gene expression data by decorrelating go graph structure. Bioinformatics, 22(13), 1600–1607.

Consortium, G. O. (2004). The gene ontology (go) database and informatics resource. Nucl. Acids Res., 32(suppl_1), D258–261.

Dai, M., Wang, P., Boyd, A. D., Kostov, G., Athey, B., Jones, E. G., Bunney,W. E., Myers, R. M., Speed, T. P., Akil, H., Watson, S. J., and Meng, F. (2005). Evolving gene/transcript definitions significantly alterthe interpretation of genechip data. Nucl. Acids Res., 33(20), e175.

Draghici, S., Khatri, P., Tarca, A. L. L., Amin, K., Done, A., Voichita, C., Georgescu, C., and Romero, R. (2007). A Systems biology approach for pathway level analysis. Genome research, 17(10), 1537–1545.

Goeman, J. J. and Buhlmann, P. (2007). Analyzing gene expression data in terms of gene sets: methodological issues. Bioinformatics, 23(8), 980–987.

Goeman, J. J., van de Geer, S. A., de Kort, F., and van Houwelingen, H. C.(2004). A global test for groups of genes: testing association with a clinical outcome. Bioinformatics, 20(1), 93–99.

Huang, D. W., Sherman, B. T., and Lempicki, R. A. (2009). Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research, 37(1), 1–13.

Lee, Y. H., Nair, S., Rousseau, E., Allison, D. B., Page, G. P., Tataranni, P. A., Bogardus, C., and Permana, P. A. (2005). Microarray profiling of isolated abdominal subcutaneous adipocytes from obese vs non-obese pima
indians: increased expression of inflammation-related genes. Diabetologia, 48(9), 1776–1783.

Mansmann, U. and Meister, R. (2005). Testing differential gene expression in functional groups. Goeman’s global test versus an ANCOVA approach. Methods of information in medicine, 44(3), 449–453.

Nam, D. and Kim, S.-Y. (2008). Gene-set approach for expression pattern
analysis. Brief Bioinform, 9(3), 189–197.

Ogata, H., Goto, S., Sato, K., Fujibuchi, W., Bono, H., and Kanehisa, M. (1999). Kegg: Kyoto encyclopedia of genes and genomes. Nucleic acids research, 27(1), 29–34.

Pico, A. R., Kelder, T., van Iersel, M. P., Hanspers, K., Conklin, B. R., and Evelo, C. (2008). Wikipathways: Pathway editing for the people. PLoS Biol, 6(7), e184+.

Salomonis, N., Hanspers, K., Zambon, A. C., Vranizan, K., Lawlor, S. C., Dahlquist, K. D., Doniger, S. W., Stuart, J., Conklin, B. R., and Pico, A. R. (2007). Genmapp 2: new features and resources for pathway analysis. BMC bioinformatics, 8, 217+.

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 knowledgebased approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America,102(43), 15545–15550.

Subramanian, A., Kuehn, H., Gould, J., Tamayo, P., and Mesirov, J. P. (2007). GSEA-P: a desktop application for gene set enrichment analysis. Bioinformatics (Oxford, England), 23(23), 3251–3253.

van Iersel, M., Kelder, T., Pico, A., Hanspers, K., Coort, S., Conklin, B., and Evelo, C. (2008). Presenting and exploring biological pathways with pathvisio. BMC Bioinformatics, 9(1), 399+.