01989nas a2200181   4500008004100000245008700041210006900128300001400197490000800211520142000219100001901639700001801658700001801676700001501694700001501709700001701724856006601741       2014                        eng d00aMolecular interactions between sugar beet and Polymyxa betae during its life cycle0 aMolecular interactions between sugar beet and Polymyxa betae dur  a244–2560 v1643 aPolymyxa betae is a biotrophic obligate sugar beet parasite that belongs to plasmodiophorids. The infection of sugar beet roots by this parasite is asymptomatic, except when it transmits Beet necrotic yellow vein virus (BNYVV), the causal agent of rhizomania. To date, there has been little work on P. betae–sugar beet molecular interactions, mainly because of the obligate nature of the parasite and also because research on rhizomania has tended to focus on the virus. In this study, we investigated these interactions through differential transcript analysis, using suppressive subtractive hybridization. The analysis included 76 P. betae and 120 sugar beet expressed sequence tags (ESTs). The expression of selected ESTs from both organisms was monitored during the protist life cycle, revealing a potential role of two P. betae proteins, profilin and a Von Willebrand factor domain-containing protein, in the early phase of infection. This study also revealed an over-expression of some sugar beet genes involved in defence, such as those encoding PR proteins, stress resistance proteins or lectins, especially during the plasmodial stage of the P. betae life cycle. In addition to providing new information on the molecular aspects of P. betae–sugar beet interactions, this study also enabled previously unknown ESTs of P. betae to be sequenced, thus enhancing our knowledge of the genome of this protist.1 aDesoignies, N.1 aCarbonell, J.1 aMoreau, J.-S.1 aConesa, A.1 aDopazo, J.1 aLegrève, A.  uhttp://onlinelibrary.wiley.com/doi/10.1111/aab.12095/abstract02142nas a2200253   4500008004100000245010200041210006900143300001100212490000700223520138600230653001501616653002401631100002401655700001801679700001601697700001401713700001501727700001601742700002001758700001501778700001701793700001501810856006301825       2008                        eng d00aBabelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments0 aBabelomics advanced functional profiling of transcriptomics prot  aW341-60 v363 a<p>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 ’de novo’ 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.</p>10ababelomics10afuntional profiling1 aAl-Shahrour, Fatima1 aCarbonell, J.1 aMinguez, P.1 aGoetz, S.1 aConesa, A.1 aTarraga, J.1 aMedina, Ignacio1 aAlloza, E.1 aMontaner, D.1 aDopazo, J.  uhttp://nar.oxfordjournals.org/content/36/suppl_2/W341.long02205nas a2200301   4500008004100000245007600041210006900117300001200186490000700198520130100205653001001506653002901516100001601545700002001561700001801581700002101599700001601620700001501636700002401651700002301675700001401698700001601712700002201728700001501750700001701765700001501782856010601797       2008                        eng d00aGEPAS, a web-based tool for microarray data analysis and interpretation0 aGEPAS a webbased tool for microarray data analysis and interpret  aW308-140 v363 a<p>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.</p>10agepas10amicroarray data analysis1 aTarraga, J.1 aMedina, Ignacio1 aCarbonell, J.1 aHuerta-Cepas, J.1 aMinguez, P.1 aAlloza, E.1 aAl-Shahrour, Fatima1 aVegas-Azcarate, S.1 aGoetz, S.1 aEscobar, P.1 aGarcia-Garcia, F.1 aConesa, A.1 aMontaner, D.1 aDopazo, J.  uhttp://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=18508806