@article {1066, title = {A novel locus for a hereditary recurrent neuropathy on chromosome 21q21.}, journal = {Neuromuscular disorders : NMD}, volume = {24}, number = {8}, year = {2014}, month = {2014 May 9}, pages = {660-5}, abstract = {Hereditary recurrent neuropathies are uncommon. Disorders with a known molecular basis falling within this group include hereditary neuropathy with liability to pressure palsies (HNPP) due to the deletion of the PMP22 gene or to mutations in this same gene, and hereditary neuralgic amyotrophy (HNA) caused by mutations in the SEPT9 gene. We report a three-generation family presenting a hereditary recurrent neuropathy without pathological changes in either PMP22 or SEPT9 genes. We performed a genome-wide mapping, which yielded a locus of 12.4Mb on chromosome 21q21. The constructed haplotype fully segregated with the disease and we found significant evidence of linkage. After mutational screening of genes located within this locus, encoding for proteins and microRNAs, as well as analysis of large deletions/insertions, we identified 71 benign polymorphisms. Our findings suggest a novel genetic locus for a recurrent hereditary neuropathy of which the molecular defect remains elusive. Our results further underscore the clinical and genetic heterogeneity of this group of neuropathies.}, issn = {1873-2364}, doi = {10.1016/j.nmd.2014.04.004}, url = {http://www.sciencedirect.com/science/article/pii/S0960896614001060$\#$}, author = {Calpena, E and Mart{\'\i}nez-Rubio, D and Arpa, J and Garc{\'\i}a-Pe{\~n}as, J J and Montaner, D. and Dopazo, J. and Palau, F and Espin{\'o}s, C} } @article {19127482, title = {Analysis of chronic lymphotic leukemia transcriptomic profile: differences between molecular subgroups}, journal = {Leuk Lymphoma}, volume = {50}, number = {1}, year = {2009}, note = {

Jantus Lewintre, Eloisa Reinoso Martin, Cristina Montaner, David Marin, Miguel Jose Terol, Maria Farras, Rosa Benet, Isabel Calvete, Juan J Dopazo, Joaquin Garcia-Conde, Javier Research Support, Non-U.S. Gov{\textquoteright}t England Leukemia \& lymphoma Leuk Lymphoma. 2009 Jan;50(1):68-79.

}, pages = {68-79}, abstract = {

B cell chronic lymphocytic leukemia (CLL) is a lymphoproliferative disorder with a variable clinical course. Patients with unmutated IgV(H) gene show a shorter progression-free and overall survival than patients with immunoglobulin heavy chain variable regions (IgV(H)) gene mutated. In addition, BCL6 mutations identify a subgroup of patients with high risk of progression. Gene expression was analysed in 36 early-stage patients using high-density microarrays. Around 150 genes differentially expressed were found according to IgV(H) mutations, whereas no difference was found according to BCL6 mutations. Functional profiling methods allowed us to distinguish KEGG and gene ontology terms showing coordinated gene expression changes across subgroups of CLL. We validated a set of differentially expressed genes according to IgV(H) status, scoring them as putative prognostic markers in CLL. Among them, CRY1, LPL, CD82 and DUSP22 are the ones with at least equal or superior performance to ZAP70 which is actually the most used surrogate marker of IgV(H) status.

}, keywords = {cancer, microarray data analysis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=19127482}, author = {Jantus Lewintre, E. and Reinoso Martin, C. and Montaner, D. and Marin, M. and Jose Terol, M. and Farras, R. and Benet, I. and Calvete, J. J. and Dopazo, J. and Garcia-Conde, J.} } @article {18515841, title = {Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, note = {

Al-Shahrour, Fatima Carbonell, Jose Minguez, Pablo Goetz, Stefan Conesa, Ana Tarraga, Joaquin Medina, Ignacio Alloza, Eva Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W341-6. Epub 2008 May 31.

}, pages = {W341-6}, abstract = {

We present a new version of Babelomics, a complete suite of web tools for the functional profiling of genome scale experiments, with new and improved methods as well as more types of functional definitions. Babelomics includes different flavours of conventional functional enrichment methods as well as more advanced gene set analysis methods that makes it a unique tool among the similar resources available. In addition to the well-known functional definitions (GO, KEGG), Babelomics includes new ones such as Biocarta pathways or text mining-derived functional terms. Regulatory modules implemented include transcriptional control (Transfac, CisRed) and other levels of regulation such as miRNA-mediated interference. Moreover, Babelomics allows for sub-selection of terms in order to test more focused hypothesis. Also gene annotation correspondence tables can be imported, which allows testing with user-defined functional modules. Finally, a tool for the {\textquoteright}de novo{\textquoteright} functional annotation of sequences has been included in the system. This allows using yet unannotated organisms in the program. Babelomics has been extensively re-engineered and now it includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. Babelomics is available at http://www.babelomics.org.

}, keywords = {babelomics, funtional profiling}, url = {http://nar.oxfordjournals.org/content/36/suppl_2/W341.long}, author = {Fatima Al-Shahrour and Carbonell, J. and Minguez, P. and Goetz, S. and A. Conesa and Tarraga, J. and Medina, Ignacio and Alloza, E. and Montaner, D. and Dopazo, J.} } @article {17597009, title = {CLEAR-test: combining inference for differential expression and variability in microarray data analysis}, journal = {J Biomed Inform}, volume = {41}, number = {1}, year = {2008}, note = {

Valls, Joan Grau, Monica Sole, Xavier Hernandez, Pilar Montaner, David Dopazo, Joaquin Peinado, Miguel A Capella, Gabriel Moreno, Victor Pujana, Miguel Angel Comparative Study Research Support, Non-U.S. Gov{\textquoteright}t United States Journal of biomedical informatics J Biomed Inform. 2008 Feb;41(1):33-45. Epub 2007 May 17.

}, pages = {33-45}, abstract = {

A common goal of microarray experiments is to detect genes that are differentially expressed under distinct experimental conditions. Several statistical tests have been proposed to determine whether the observed changes in gene expression are significant. The t-test assigns a score to each gene on the basis of changes in its expression relative to its estimated variability, in such a way that genes with a higher score (in absolute values) are more likely to be significant. Most variants of the t-test use the complete set of genes to influence the variance estimate for each single gene. However, no inference is made in terms of the variability itself. Here, we highlight the problem of low observed variances in the t-test, when genes with relatively small changes are declared differentially expressed. Alternatively, the z-test could be used although, unlike the t-test, it can declare differentially expressed genes with high observed variances. To overcome this, we propose to combine the z-test, which focuses on large changes, with a chi(2) test to evaluate variability. We call this procedure CLEAR-test and we provide a combined p-value that offers a compromise between both aspects. Analysis of three publicly available microarray datasets reveals the greater performance of the CLEAR-test relative to the t-test and alternative methods. Finally, empirical and simulated data analyses demonstrate the greater reproducibility and statistical power of the CLEAR-test and z-test with respect to current alternative methods. In addition, the CLEAR-test improves the z-test by capturing reproducible genes with high variability.

}, keywords = {*Algorithms Artificial Intelligence *Data Interpretation, Statistical Gene Expression Profiling/*methods Gene Expression Regulation/*physiology Oligonucleotide Array Sequence Analysis/*methods Proteome/*metabolism Signal Transduction/*physiology}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17597009}, author = {Valls, J. and Grau, M. and Sole, X. and Hernandez, P. and Montaner, D. and Dopazo, J. and Peinado, M. A. and Capella, G. and Moreno, V. and Pujana, M. A.} } @article {18652888, title = {Direct functional assessment of the composite phenotype through multivariate projection strategies}, journal = {Genomics}, volume = {92}, number = {6}, year = {2008}, note = {

Conesa, Ana Bro, Rasmus Garcia-Garcia, Francisco Prats, Jose Manuel Gotz, Stefan Kjeldahl, Karin Montaner, David Dopazo, Joaquin Evaluation Studies Research Support, Non-U.S. Gov{\textquoteright}t United States Genomics Genomics. 2008 Dec;92(6):373-83. Epub 2008 Sep 13.

}, pages = {373-83}, abstract = {

We present a novel approach for the analysis of transcriptomics data that integrates functional annotation of gene sets with expression values in a multivariate fashion, and directly assesses the relation of functional features to a multivariate space of response phenotypical variables. Multivariate projection methods are used to obtain new correlated variables for a set of genes that share a given function. These new functional variables are then related to the response variables of interest. The analysis of the principal directions of the multivariate regression allows for the identification of gene function features correlated with the phenotype. Two different transcriptomics studies are used to illustrate the statistical and interpretative aspects of the methodology. We demonstrate the superiority of the proposed method over equivalent approaches.

}, keywords = {Breast Neoplasms/genetics Computational Biology/*methods Databases, Genetic Female Gene Expression Profiling/*statistics \& numerical data Humans Mathematical Computing Multivariate Analysis Phenotype}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18652888}, author = {A. Conesa and Bro, R. and Garcia-Garcia, F. and Prats, J. M. and Gotz, S. and Kjeldahl, K. and Montaner, D. and Dopazo, J.} } @article {18508806, title = {GEPAS, a web-based tool for microarray data analysis and interpretation}, journal = {Nucleic Acids Res}, volume = {36}, year = {2008}, note = {

Tarraga, Joaquin Medina, Ignacio Carbonell, Jose Huerta-Cepas, Jaime Minguez, Pablo Alloza, Eva Al-Shahrour, Fatima Vegas-Azcarate, Susana Goetz, Stefan Escobar, Pablo Garcia-Garcia, Francisco Conesa, Ana Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W308-14. Epub 2008 May 28.

}, pages = {W308-14}, abstract = {

Gene Expression Profile Analysis Suite (GEPAS) is one of the most complete and extensively used web-based packages for microarray data analysis. During its more than 5 years of activity it has continuously been updated to keep pace with the state-of-the-art in the changing microarray data analysis arena. GEPAS offers diverse analysis options that include well established as well as novel algorithms for normalization, gene selection, class prediction, clustering and functional profiling of the experiment. New options for time-course (or dose-response) experiments, microarray-based class prediction, new clustering methods and new tests for differential expression have been included. The new pipeliner module allows automating the execution of sequential analysis steps by means of a simple but powerful graphic interface. An extensive re-engineering of GEPAS has been carried out which includes the use of web services and Web 2.0 technology features, a new user interface with persistent sessions and a new extended database of gene identifiers. GEPAS is nowadays the most quoted web tool in its field and it is extensively used by researchers of many countries and its records indicate an average usage rate of 500 experiments per day. GEPAS, is available at http://www.gepas.org.

}, keywords = {gepas, microarray data analysis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=18508806}, author = {Tarraga, J. and Medina, Ignacio and Carbonell, J. and Huerta-Cepas, J. and Minguez, P. and Alloza, E. and Fatima Al-Shahrour and Vegas-Azcarate, S. and Goetz, S. and Escobar, P. and Garcia-Garcia, F. and A. Conesa and Montaner, D. and Dopazo, J.} } @article {17873908, title = {Molecular profiling related to poor prognosis in thyroid carcinoma. Combining gene expression data and biological information}, journal = {Oncogene}, volume = {27}, number = {11}, year = {2008}, note = {

Montero-Conde, C Martin-Campos, J M Lerma, E Gimenez, G Martinez-Guitarte, J L Combalia, N Montaner, D Matias-Guiu, X Dopazo, J de Leiva, A Robledo, M Mauricio, D Research Support, Non-U.S. Gov{\textquoteright}t England Oncogene Oncogene. 2008 Mar 6;27(11):1554-61. Epub 2007 Sep 17.

}, pages = {1554-61}, abstract = {

Undifferentiated and poorly differentiated thyroid tumors are responsible for more than half of thyroid cancer patient deaths in spite of their low incidence. Conventional treatments do not obtain substantial benefits, and the lack of alternative approaches limits patient survival. Additionally, the absence of prognostic markers for well-differentiated tumors complicates patient-specific treatments and favors the progression of recurrent forms. In order to recognize the molecular basis involved in tumor dedifferentiation and identify potential markers for thyroid cancer prognosis prediction, we analysed the expression profile of 44 thyroid primary tumors with different degrees of dedifferentiation and aggressiveness using cDNA microarrays. Transcriptome comparison of dedifferentiated and well-differentiated thyroid tumors identified 1031 genes with \>2-fold difference in absolute values and false discovery rate of \<0.15. According to known molecular interaction and reaction networks, the products of these genes were mainly clustered in the MAPkinase signaling pathway, the TGF-beta signaling pathway, focal adhesion and cell motility, activation of actin polymerization and cell cycle. An exhaustive search in several databases allowed us to identify various members of the matrix metalloproteinase, melanoma antigen A and collagen gene families within the upregulated gene set. We also identified a prognosis classifier comprising just 30 transcripts with an overall accuracy of 95\%. These findings may clarify the molecular mechanisms involved in thyroid tumor dedifferentiation and provide a potential prognosis predictor as well as targets for new therapies.

}, keywords = {Adenoma/genetics/metabolism/pathology Adolescent Adult Aged Carcinoma/genetics/metabolism/pathology Carcinoma, Biological/*genetics/metabolism, Neoplasm/genetics/metabolism Reverse Transcriptase Polymerase Chain Reaction Signal Transduction Thyroid Neoplasms/classification/*genetics/metabolism Tumor Markers, Neoplastic Humans Male Middle Aged *Oligonucleotide Array Sequence Analysis Prognosis RNA, Papillary/genetics/metabolism/pathology Cell Differentiation Female *Gene Expression Profiling *Gene Expression Regulation}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17873908}, author = {Montero-Conde, C. and Martin-Campos, J. M. and Lerma, E. and Gimenez, G. and Martinez-Guitarte, J. L. and Combalia, N. and Montaner, D. and Matias-Guiu, X. and Dopazo, J. and de Leiva, A. and M. Robledo and Mauricio, D.} } @article {17584915, title = {Evidence for systems-level molecular mechanisms of tumorigenesis}, journal = {BMC Genomics}, volume = {8}, year = {2007}, note = {Hernandez, Pilar Huerta-Cepas, Jaime Montaner, David Al-Shahrour, Fatima Valls, Joan Gomez, Laia Capella, Gabriel Dopazo, Joaquin Pujana, Miguel Angel Research Support, Non-U.S. Gov{\textquoteright}t England BMC genomics BMC Genomics. 2007 Jun 20;8:185.}, pages = {185}, abstract = {BACKGROUND: Cancer arises from the consecutive acquisition of genetic alterations. Increasing evidence suggests that as a consequence of these alterations, molecular interactions are reprogrammed in the context of highly connected and regulated cellular networks. Coordinated reprogramming would allow the cell to acquire the capabilities for malignant growth. RESULTS: Here, we determine the coordinated function of cancer gene products (i.e., proteins encoded by differentially expressed genes in tumors relative to healthy tissue counterparts, hereafter referred to as "CGPs") defined as their topological properties and organization in the interactome network. We show that CGPs are central to information exchange and propagation and that they are specifically organized to promote tumorigenesis. Centrality is identified by both local (degree) and global (betweenness and closeness) measures, and systematically appears in down-regulated CGPs. Up-regulated CGPs do not consistently exhibit centrality, but both types of cancer products determine the overall integrity of the network structure. In addition to centrality, down-regulated CGPs show topological association that correlates with common biological processes and pathways involved in tumorigenesis. CONCLUSION: Given the current limited coverage of the human interactome, this study proposes that tumorigenesis takes place in a specific and organized way at the molecular systems-level and suggests a model that comprises the precise down-regulation of groups of topologically-associated proteins involved in particular functions, orchestrated with the up-regulation of specific proteins.}, keywords = {*Cell Transformation, Biological Models, Genetic Models, Messenger/metabolism Signal Transduction Systems Biology, Neoplastic *Gene Expression Profiling *Gene Expression Regulation, Neoplastic Humans Male Models, Statistical Neoplasm Proteins/*physiology Neoplasms/etiology/*genetics Prostatic Neoplasms/genetics Protein Interaction Mapping RNA}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17584915}, author = {Hernandez, P. and Huerta-Cepas, J. and Montaner, D. and Fatima Al-Shahrour and Valls, J. and Gomez, L. and Capella, G. and Dopazo, J. and Pujana, M. A.} } @article {17478504, 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}, number = {Web Server issue}, year = {2007}, note = {

Al-Shahrour, Fatima Minguez, Pablo Tarraga, Joaquin Medina, Ignacio Alloza, Eva Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W91-6. Epub 2007 May 3.

}, 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 = {babelomics, functional enrichment analysys}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17478504}, author = {Fatima Al-Shahrour and Minguez, P. and Tarraga, J. and Medina, Ignacio and Alloza, E. and Montaner, D. and Dopazo, J.} } @article {17407596, title = {From genes to functional classes in the study of biological systems}, journal = {BMC Bioinformatics}, volume = {8}, year = {2007}, note = {

Al-Shahrour, Fatima Arbiza, Leonardo Dopazo, Hernan Huerta-Cepas, Jaime Minguez, Pablo Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England BMC bioinformatics BMC Bioinformatics. 2007 Apr 3;8:114.

}, pages = {114}, abstract = {

BACKGROUND: With the popularization of high-throughput techniques, the need for procedures that help in the biological interpretation of results has increased enormously. Recently, new procedures inspired in systems biology criteria have started to be developed. RESULTS: Here we present FatiScan, a web-based program which implements a threshold-independent test for the functional interpretation of large-scale experiments that does not depend on the pre-selection of genes based on the multiple application of independent tests to each gene. The test implemented aims to directly test the behaviour of blocks of functionally related genes, instead of focusing on single genes. In addition, the test does not depend on the type of the data used for obtaining significance values, and consequently different types of biologically informative terms (gene ontology, pathways, functional motifs, transcription factor binding sites or regulatory sites from CisRed) can be applied to different classes of genome-scale studies. We exemplify its application in microarray gene expression, evolution and interactomics. CONCLUSION: Methods for gene set enrichment which, in addition, are independent from the original data and experimental design constitute a promising alternative for the functional profiling of genome-scale experiments. A web server that performs the test described and other similar ones can be found at: http://www.babelomics.org.

}, keywords = {Algorithms Chromosome Mapping/*methods Computer Simulation Gene Expression Profiling/methods *Models, babelomics, Biological Multigene Family/*physiology Signal Transduction/*physiology *Software Systems Biology/*methods *User-Computer Interface}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17407596}, author = {Fatima Al-Shahrour and Arbiza, L. and H. Dopazo and Huerta-Cepas, J. and Minguez, P. and Montaner, D. and Dopazo, J.} } @article {17597935, title = {Functional profiling and gene expression analysis of chromosomal copy number alterations}, journal = {Bioinformation}, volume = {1}, number = {10}, year = {2007}, note = {

Conde, Lucia Montaner, David Burguet-Castell, Jordi Tarraga, Joaquin Al-Shahrour, Fatima Dopazo, Joaquin Singapore Bioinformation Bioinformation. 2007 Apr 10;1(10):432-5.

}, pages = {432-5}, abstract = {

Contrarily to the traditional view in which only one or a few key genes were supposed to be the causative factors of diseases, we discuss the importance of considering groups of functionally related genes in the study of pathologies characterised by chromosomal copy number alterations. Recent observations have reported the existence of regions in higher eukaryotic chromosomes (including humans) containing genes of related function that show a high degree of coregulation. Copy number alterations will consequently affect to clusters of functionally related genes, which will be the final causative agents of the diseased phenotype, in many cases. Therefore, we propose that the functional profiling of the regions affected by copy number alterations must be an important aspect to take into account in the understanding of this type of pathologies. To illustrate this, we present an integrated study of DNA copy number variations, gene expression along with the functional profiling of chromosomal regions in a case of multiple myeloma.

}, keywords = {babelomics}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17597935}, author = {L. Conde and Montaner, D. and Burguet-Castell, J. and Tarraga, J. and Fatima Al-Shahrour and Dopazo, J.} } @article {17855415, title = {Functional profiling of microarray experiments using text-mining derived bioentities}, journal = {Bioinformatics}, volume = {23}, number = {22}, year = {2007}, note = {

Minguez, Pablo Al-Shahrour, Fatima Montaner, David Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Bioinformatics (Oxford, England) Bioinformatics. 2007 Nov 15;23(22):3098-9. Epub 2007 Sep 13.

}, pages = {3098-9}, abstract = {

MOTIVATION: The increasing use of microarray technologies brought about a parallel demand in methods for the functional interpretation of the results. Beyond the conventional functional annotations for genes, such as gene ontology, pathways, etc. other sources of information are still to be exploited. Text-mining methods allow extracting informative terms (bioentities) with different functional, chemical, clinical, etc. meanings, that can be associated to genes. We show how to use these associations within an appropriate statistical framework and how to apply them through easy-to-use, web-based environments to the functional interpretation of microarray experiments. Functional enrichment and gene set enrichment tests using bioentities are presented.

}, keywords = {Artificial Intelligence *Databases, babelomics, Protein Gene Expression Profiling/*methods Information Storage and Retrieval/*methods *Natural Language Processing Proteins/*classification/*metabolism Research/*methods Systems Integration}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17855415}, author = {Minguez, P. and Fatima Al-Shahrour and Montaner, D. and Dopazo, J.} } @article {17468499, title = {ISACGH: a web-based environment for the analysis of Array CGH and gene expression which includes functional profiling}, journal = {Nucleic Acids Res}, volume = {35}, number = {Web Server issue}, year = {2007}, note = {Conde, Lucia Montaner, David Burguet-Castell, Jordi Tarraga, Joaquin Medina, Ignacio Al-Shahrour, Fatima Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2007 Jul;35(Web Server issue):W81-5. Epub 2007 Apr 27.}, pages = {W81-5}, abstract = {We present the ISACGH, a web-based system that allows for the combination of genomic data with gene expression values and provides different options for functional profiling of the regions found. Several visualization options offer a convenient representation of the results. Different efficient methods for accurate estimation of genomic copy number from array-CGH hybridization data have been included in the program. Moreover, the connection to the gene expression analysis package GEPAS allows the use of different facilities for data pre-processing and analysis. A DAS server allows exporting the results to the Ensembl viewer where contextual genomic information can be obtained. The program is freely available at: http://isacgh.bioinfo.cipf.es or within http://www.gepas.org.}, keywords = {Animals Cluster Analysis Computational Biology/*methods Computer Graphics Gene Expression Profiling/*methods Humans Internet Models, Genetic *Nucleic Acid Hybridization Oligonucleotide Array Sequence Analysis/*methods Programming Languages *Software Systems Integration User-Computer Interface}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=17468499}, author = {L. Conde and Montaner, D. and Burguet-Castell, J. and Tarraga, J. and Medina, Ignacio and Fatima Al-Shahrour and Dopazo, J.} } @inbook {680, title = {New Trends in the Analysis of Functional Genomic Data}, booktitle = {Progress in Industrial Mathematics at ECMI 2006}, volume = {12}, year = {2007}, pages = {576-580}, publisher = {Springer}, organization = {Springer}, address = {Berlin}, issn = {978-3-540-71991-5}, doi = {10.1007/978-3-540-71992-2_94}, url = {http://www.springerlink.com/content/m62p07r8111004vr/}, author = {Montaner, D. and Fatima Al-Shahrour and Dopazo, J.} } @article {17138587, title = {Prophet, a web-based tool for class prediction using microarray data}, journal = {Bioinformatics}, volume = {23}, number = {3}, year = {2007}, note = {

Medina, Ignacio Montaner, David Tarraga, Joaquin Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Bioinformatics (Oxford, England) Bioinformatics. 2007 Feb 1;23(3):390-1. Epub 2006 Nov 30.

}, pages = {390-1}, abstract = {

Sample classification and class prediction is the aim of many gene expression studies. We present a web-based application, Prophet, which builds prediction rules and allows using them for further sample classification. Prophet automatically chooses the best classifier, along with the optimal selection of genes, using a strategy that renders unbiased cross-validated errors. Prophet is linked to different microarray data analysis modules, and includes a unique feature: the possibility of performing the functional interpretation of the molecular signature found. Availability: Prophet can be found at the URL http://prophet.bioinfo.cipf.es/ or within the GEPAS package at http://www.gepas.org/ Supplementary information: http://gepas.bioinfo.cipf.es/tutorial/prophet.html.

}, keywords = {babelomics, gepas, predictors}, url = {http://bioinformatics.oxfordjournals.org/cgi/content/full/23/3/390?view=long\&pmid=17138587}, author = {Medina, Ignacio and Montaner, D. and Tarraga, J. and Dopazo, J.} } @article {16845052, title = {BABELOMICS: a systems biology perspective in the functional annotation of genome-scale experiments}, journal = {Nucleic Acids Res}, volume = {34}, year = {2006}, note = {

Al-Shahrour, Fatima Minguez, Pablo Tarraga, Joaquin Montaner, David Alloza, Eva Vaquerizas, Juan M Conde, Lucia Blaschke, Christian Vera, Javier Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W472-6.

}, pages = {W472-6}, abstract = {

We present a new version of Babelomics, a complete suite of web tools for functional analysis of genome-scale experiments, with new and improved tools. New functionally relevant terms have been included such as CisRed motifs or bioentities obtained by text-mining procedures. An improved indexing has considerably speeded up several of the modules. An improved version of the FatiScan method for studying the coordinate behaviour of groups of functionally related genes is presented, along with a similar tool, the Gene Set Enrichment Analysis. Babelomics is now more oriented to test systems biology inspired hypotheses. Babelomics can be found at http://www.babelomics.org.

}, keywords = {babelomics, functional profiling}, url = {http://nar.oxfordjournals.org/content/34/suppl_2/W472.long}, author = {Fatima Al-Shahrour and Minguez, P. and Tarraga, J. and Montaner, D. and Alloza, E. and Vaquerizas, J. M. and L. Conde and Blaschke, C. and Vera, J. and Dopazo, J.} } @article {16845056, title = {Next station in microarray data analysis: GEPAS}, journal = {Nucleic Acids Res}, volume = {34}, year = {2006}, note = {

Montaner, David Tarraga, Joaquin Huerta-Cepas, Jaime Burguet, Jordi Vaquerizas, Juan M Conde, Lucia Minguez, Pablo Vera, Javier Mukherjee, Sach Valls, Joan Pujana, Miguel A G Alloza, Eva Herrero, Javier Al-Shahrour, Fatima Dopazo, Joaquin Research Support, Non-U.S. Gov{\textquoteright}t England Nucleic acids research Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W486-91.

}, pages = {W486-91}, abstract = {

The Gene Expression Profile Analysis Suite (GEPAS) has been running for more than four years. During this time it has evolved to keep pace with the new interests and trends in the still changing world of microarray data analysis. GEPAS has been designed to provide an intuitive although powerful web-based interface that offers diverse analysis options from the early step of preprocessing (normalization of Affymetrix and two-colour microarray experiments and other preprocessing options), to the final step of the functional annotation of the experiment (using Gene Ontology, pathways, PubMed abstracts etc.), and include different possibilities for clustering, gene selection, class prediction and array-comparative genomic hybridization management. GEPAS is extensively used by researchers of many countries and its records indicate an average usage rate of 400 experiments per day. The web-based pipeline for microarray gene expression data, GEPAS, is available at http://www.gepas.org.

}, keywords = {gepas, microarray data analysis}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=16845056}, author = {Montaner, D. and Tarraga, J. and Huerta-Cepas, J. and Burguet, J. and Vaquerizas, J. M. and L. Conde and Minguez, P. and Vera, J. and Mukherjee, S. and Valls, J. and Pujana, M. A. and Alloza, E. and Herrero, J. and Fatima Al-Shahrour and Dopazo, J.} } @article {16584746, title = {Selective pressures at a codon-level predict deleterious mutations in human disease genes}, journal = {J Mol Biol}, volume = {358}, number = {5}, year = {2006}, note = {Arbiza, Leonardo Duchi, Serena Montaner, David Burguet, Jordi Pantoja-Uceda, David Pineda-Lucena, Antonio Dopazo, Joaquin Dopazo, Hernan Research Support, Non-U.S. Gov{\textquoteright}t England Journal of molecular biology J Mol Biol. 2006 May 19;358(5):1390-404. Epub 2006 Mar 15.}, pages = {1390-404}, abstract = {Deleterious mutations affecting biological function of proteins are constantly being rejected by purifying selection from the gene pool. The non-synonymous/synonymous substitution rate ratio (omega) is a measure of selective pressure on amino acid replacement mutations for protein-coding genes. Different methods have been developed in order to predict non-synonymous changes affecting gene function. However, none has considered the estimation of selective constraints acting on protein residues. Here, we have used codon-based maximum likelihood models in order to estimate the selective pressures on the individual amino acid residues of a well-known model protein: p53. We demonstrate that the number of residues under strong purifying selection in p53 is much higher than those that are strictly conserved during the evolution of the species. In agreement with theoretical expectations, residues that have been noted to be of structural relevance, or in direct association with DNA, were among those showing the highest signals of purifying selection. Conversely, those changing according to a neutral, or nearly neutral mode of evolution, were observed to be irrelevant for protein function. Finally, using more than 40 human disease genes, we demonstrate that residues evolving under strong selective pressures (omega<0.1) are significantly associated (p<0.01) with human disease. We hypothesize that non-synonymous change on amino acids showing omega<0.1 will most likely affect protein function. The application of this evolutionary prediction at a genomic scale will provide an a priori hypothesis of the phenotypic effect of non-synonymous coding single nucleotide polymorphisms (SNPs) in the human genome.}, keywords = {Amino Acid Sequence Amino Acid Substitution Codon/*genetics Databases, Genetic Evolution, Genetic Models, Human Humans Models, Inborn/*genetics Genome, Molecular Genes, Molecular Molecular Sequence Data *Mutation Neoplasms/genetics Proteins/genetics *Selection (Genetics) Tumor Suppressor Protein p53/chemistry/genetics, p53 Genetic Diseases}, url = {http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve\&db=PubMed\&dopt=Citation\&list_uids=16584746}, author = {Arbiza, L. and Duchi, S. and Montaner, D. and Burguet, J. and Pantoja-Uceda, D. and Pineda-Lucena, A. and Dopazo, J. and H. Dopazo} }