@article {583, title = {Gene set-based analysis of polymorphisms: finding pathways or biological processes associated to traits in genome-wide association studies.}, journal = {Nucleic Acids Res}, volume = {37}, year = {2009}, month = {2009 Jul}, pages = {W340-4}, abstract = {

Genome-wide association studies have become a popular strategy to find associations of genes to traits of interest. Despite the high-resolution available today to carry out genotyping studies, the success of its application in real studies has been limited by the testing strategy used. As an alternative to brute force solutions involving the use of very large cohorts, we propose the use of the Gene Set Analysis (GSA), a different analysis strategy based on testing the association of modules of functionally related genes. We show here how the Gene Set-based Analysis of Polymorphisms (GeSBAP), which is a simple implementation of the GSA strategy for the analysis of genome-wide association studies, provides a significant increase in the power testing for this type of studies. GeSBAP is freely available at http://bioinfo.cipf.es/gesbap/.

}, keywords = {Biological Phenomena, Breast Neoplasms, Female, Genes, Genetic Variation, Genome-Wide Association Study, Humans, Polymorphism, Single Nucleotide, Software, User-Computer Interface}, issn = {1362-4962}, doi = {10.1093/nar/gkp481}, author = {Medina, Ignacio and Montaner, David and Bonifaci, N{\'u}ria and Pujana, Miguel Angel and Carbonell, Jos{\'e} and T{\'a}rraga, Joaqu{\'\i}n and Al-Shahrour, F{\'a}tima and Dopazo, Joaquin} } @article {594, title = {High-throughput functional annotation and data mining with the Blast2GO suite.}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Jun}, pages = {3420-35}, abstract = {

Functional genomics technologies have been widely adopted in the biological research of both model and non-model species. An efficient functional annotation of DNA or protein sequences is a major requirement for the successful application of these approaches as functional information on gene products is often the key to the interpretation of experimental results. Therefore, there is an increasing need for bioinformatics resources which are able to cope with large amount of sequence data, produce valuable annotation results and are easily accessible to laboratories where functional genomics projects are being undertaken. We present the Blast2GO suite as an integrated and biologist-oriented solution for the high-throughput and automatic functional annotation of DNA or protein sequences based on the Gene Ontology vocabulary. The most outstanding Blast2GO features are: (i) the combination of various annotation strategies and tools controlling type and intensity of annotation, (ii) the numerous graphical features such as the interactive GO-graph visualization for gene-set function profiling or descriptive charts, (iii) the general sequence management features and (iv) high-throughput capabilities. We used the Blast2GO framework to carry out a detailed analysis of annotation behaviour through homology transfer and its impact in functional genomics research. Our aim is to offer biologists useful information to take into account when addressing the task of functionally characterizing their sequence data.

}, keywords = {Animals, Computational Biology, Computer Graphics, Databases, Genetic, Expressed Sequence Tags, Genes, Genomics, Sequence Analysis, DNA, Sequence Analysis, Protein, Software, Vocabulary, Controlled}, issn = {1362-4962}, doi = {10.1093/nar/gkn176}, author = {G{\"o}tz, Stefan and Garc{\'\i}a-G{\'o}mez, Juan Miguel and Terol, Javier and Williams, Tim D and Nagaraj, Shivashankar H and Nueda, Maria Jos{\'e} and Robles, Montserrat and Talon, Manuel and Dopazo, Joaquin and Conesa, Ana} } @article {598, title = {PhylomeDB: a database for genome-wide collections of gene phylogenies.}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, month = {2008 Jan}, pages = {D491-6}, abstract = {

The complete collection of evolutionary histories of all genes in a genome, also known as phylome, constitutes a valuable source of information. The reconstruction of phylomes has been previously prevented by large demands of time and computer power, but is now feasible thanks to recent developments in computers and algorithms. To provide a publicly available repository of complete phylomes that allows researchers to access and store large-scale phylogenomic analyses, we have developed PhylomeDB. PhylomeDB is a database of complete phylomes derived for different genomes within a specific taxonomic range. All phylomes in the database are built using a high-quality phylogenetic pipeline that includes evolutionary model testing and alignment trimming phases. For each genome, PhylomeDB provides the alignments, phylogentic trees and tree-based orthology predictions for every single encoded protein. The current version of PhylomeDB includes the phylomes of Human, the yeast Saccharomyces cerevisiae and the bacterium Escherichia coli, comprising a total of 32 289 seed sequences with their corresponding alignments and 172 324 phylogenetic trees. PhylomeDB can be publicly accessed at http://phylomedb.bioinfo.cipf.es.

}, keywords = {Base Sequence, Escherichia coli, Genes, Genomics, History, Ancient, Humans, Phylogeny, Proteins, Saccharomyces cerevisiae, Sequence Alignment}, issn = {1362-4962}, doi = {10.1093/nar/gkm899}, author = {Huerta-Cepas, Jaime and Bueno, Anibal and Dopazo, Joaquin and Gabald{\'o}n, Toni} } @article {605, title = {FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.}, journal = {Nucleic Acids Res}, volume = {35}, year = {2007}, month = {2007 Jul}, pages = {W91-6}, abstract = {

The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org.

}, keywords = {Amino Acid Motifs, Animals, Binding Sites, Computational Biology, Gene Expression Profiling, Genes, Genomics, Humans, Internet, Oligonucleotide Array Sequence Analysis, Programming Languages, Software, Systems Integration, Transcription Factors}, issn = {1362-4962}, doi = {10.1093/nar/gkm260}, author = {Al-Shahrour, F{\'a}tima and Minguez, Pablo and T{\'a}rraga, Joaqu{\'\i}n and Medina, Ignacio and Alloza, Eva and Montaner, David and Dopazo, Joaquin} }