G. V. Glazko and F. Emmert-streib, Unite and conquer: univariate and multivariate approaches for finding differentially expressed gene sets, Bioinformatics, vol.25, issue.18, pp.2348-2354, 2009.
DOI : 10.1093/bioinformatics/btp406

P. Khatri, M. Sirota, and A. J. Butte, Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges, PLoS Computational Biology, vol.23, issue.2, p.1002375, 2012.
DOI : 10.1371/journal.pcbi.1002375.s006

M. Kanehisa, S. Goto, Y. Sato, M. Furumichi, and M. Tanabe, KEGG for integration and interpretation of large-scale molecular data sets, Nucleic Acids Research, vol.40, issue.D1, pp.109-114, 2012.
DOI : 10.1093/nar/gkr988

S. Hunter, P. Jones, A. Mitchell, R. Apweiler, T. K. Attwood et al., InterPro in 2011: new developments in the family and domain prediction database, Nucleic Acids Research, vol.40, issue.D1, pp.306-312, 2012.
DOI : 10.1093/nar/gkr948

URL : https://hal.archives-ouvertes.fr/hal-00697960

G. Consortium, Gene Ontology Annotations and Resources, Nucleic Acids Research, vol.41, issue.D1, pp.530-535, 2013.
DOI : 10.1093/nar/gks1050

W. Huang-da, B. T. Sherman, and R. A. Lempicki, Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nature Protocols, vol.99, issue.1, pp.44-57, 2009.
DOI : 10.1038/nprot.2008.211

W. Huang-da, 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, issue.1, pp.1-13, 2009.
DOI : 10.1093/nar/gkn923

J. Reimand, T. Arak, and J. Vilo, g:Profiler--a web server for functional interpretation of gene lists (2011 update), Nucleic Acids Research, vol.39, issue.suppl, pp.307-315, 2011.
DOI : 10.1093/nar/gkr378

J. Reimand, M. Kull, H. Peterson, J. Hansen, and J. Vilo, g:Profiler--a web-based toolset for functional profiling of gene lists from large-scale experiments, Nucleic Acids Research, vol.35, issue.Web Server, pp.193-200, 2007.
DOI : 10.1093/nar/gkm226

E. Eden, R. Navon, I. Steinfeld, D. Lipson, and Z. Yakhini, GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists, BMC Bioinformatics, vol.10, issue.1, p.48, 2009.
DOI : 10.1186/1471-2105-10-48

B. R. Zeeberg, H. Qin, S. Narasimhan, M. Sunshine, H. Cao et al., High-Throughput GoMiner, an 'industrial-strength' integrative gene ontology tool for interpretation of multiplemicroarray experiments, with application to studies of common variable immune deficiency (CVID), BMC Bioinformatics, vol.6, issue.1, p.168, 2005.
DOI : 10.1186/1471-2105-6-168

I. Medina, J. Carbonell, L. Pulido, S. C. Madeira, S. Goetz et al., Babelomics: an integrative platform for the analysis of transcriptomics, proteomics and genomic data with advanced functional profiling, Nucleic Acids Research, vol.38, issue.Web Server, pp.210-213, 2010.
DOI : 10.1093/nar/gkq388

D. Tabas-madrid, R. Nogales-cadenas, and A. Montano, GeneCodis3: a non-redundant and modular enrichment analysis tool for functional genomics, Nucleic Acids Research, vol.40, issue.W1, pp.478-483, 2012.
DOI : 10.1093/nar/gks402

C. Trapnell, D. G. Hendrickson, M. Sauvageau, L. Goff, J. L. Rinn et al., Differential analysis of gene regulation at transcript resolution with RNA-seq, Nature Biotechnology, vol.31, issue.1, pp.46-53, 2012.
DOI : 10.1016/j.cell.2012.06.041

C. Trapnell, A. Roberts, L. Goff, G. Pertea, D. Kim et al., Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks, Nature Protocols, vol.7, issue.3, pp.562-578, 2012.
DOI : 10.1038/nbt0710-691

M. D. Robinson, D. J. Mccarthy, and G. K. Smyth, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, issue.1, pp.139-140, 2010.
DOI : 10.1093/bioinformatics/btp616

S. Anders and W. Huber, Differential expression analysis for sequence count data, Genome Biology, vol.11, issue.10, p.106, 2010.
DOI : 10.1186/gb-2010-11-10-r106

Y. Benjamini and D. Yekutieli, The control of the false discovery rate in multiple testing under dependency, Ann. Stat, vol.29, pp.1165-1188, 2001.

R. A. Uribe, T. Kwon, E. M. Marcotte, and J. M. Gross, Id2a functions to limit Notch pathway activity and thereby influence the transition from proliferation to differentiation of retinoblasts during zebrafish retinogenesis, Developmental Biology, vol.371, issue.2, pp.280-292, 2012.
DOI : 10.1016/j.ydbio.2012.08.032

D. L. Eizirik, M. Sammeth, T. Bouckenooghe, G. Bottu, G. Sisino et al., The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines, PLoS Genetics, vol.6, issue.3, p.1002552, 2012.
DOI : 10.1371/journal.pgen.1002552.s011

P. Flicek, I. Ahmed, M. R. Amode, D. Barrell, K. Beal et al., Ensembl 2013, Nucleic Acids Research, vol.41, issue.D1, pp.48-55, 2013.
DOI : 10.1093/nar/gks1236

URL : http://doi.org/10.1093/nar/gks1236

G. Consortium, Creating the Gene Ontology Resource: Design and Implementation, Genome Research, vol.11, issue.8, pp.1425-1433, 2001.
DOI : 10.1101/gr.180801

G. Consortium, The Gene Ontology: enhancements for 2011, Nucleic Acids Research, vol.40, issue.D1, pp.559-564, 2012.
DOI : 10.1093/nar/gkr1028

M. A. Harris, J. Clark, A. Ireland, J. Lomax, M. Ashburner et al., The gene ontology (GO) database and informatics resource, Nucleic Acids Res, vol.32, pp.258-261, 2004.