MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

<p>Abstract</p> <p>Background</p> <p>Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill.</p> <p>Description</p> <p>MADIBA (MicroArray Data Interface for Biological Annotation) facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for <it>Plasmodium</it>, rice and <it>Arabidopsis</it>. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied.</p> <p>Conclusion</p> <p>MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the <it>Plasmodium </it>life cycle, and salt stress treatments of <it>Arabidopsis </it>and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA. </p

Inférence fonctionnelle et prédiction de voies métaboliques (application à la bactérie fixatrice d'azote Sinorhizobium meliloti)

TOULOUSE3-BU Sciences (315552104) / SudocSudocFranceF

Characterization of PfMyb1 transcription factor during erythrocytic development of 3D7 and F12 Plasmodium falciparum clones

International audienc

Nitric oxide participates in the complex interplay of defense-related signaling pathways controlling disease resistance to Sclerotinia sclerotiorum in Arabidopsis thaliana.

International audienceStudies of the interaction between Arabidopsis thaliana and the necrotrophic fungal pathogen Sclerotinia sclerotiorum have been hampered by the extreme susceptibility of this model plant to the fungus. In addition, analyses of the plant defense response suggested the implication of a complex interplay of hormonal and signaling pathways. To get a deeper insight into this host-pathogen interaction, we first analyzed the natural variation in Arabidopsis for resistance to S. sclerotiorum. The results revealed a large variation of resistance and susceptibility in Arabidopsis, with some ecotypes, such as Ws-4, Col-0, and Rbz-1, being strongly resistant, and others, such as Shahdara, Ita-0, and Cvi-0, exhibiting an extreme susceptibility. The role of different signaling pathways in resistance was then determined by assessing the symptoms of mutants affected in the perception, production, or transduction of hormonal signals after inoculation with S. sclerotiorum. This analysis led to the conclusions that i) signaling of inducible defenses is predominantly mediated by jasmonic acid and abscisic acid, influenced by ethylene, and independent of salicylic acid; and ii) nitric oxide (NO) and reactive oxygen species are important signals required for plant resistance to S. sclerotiorum. Defense gene expression analysis supported the specific role of NO in defense activation

MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters-4

Aerobic glycolysis was the most significant term. The DAG was reduced to show only the terms that are most relevant to glucose metabolism. The grey ellipses contain the genes that are annotated to the connected GO term and the colour of the GO terms indicates different levels of significance, as indicated by the legend.<p><b>Copyright information:</b></p><p>Taken from "MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters"</p><p>http://www.biomedcentral.com/1471-2164/9/105</p><p>BMC Genomics 2008;9():105-105.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2277412.</p><p></p

MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters-1

Aerobic glycolysis was the most significant term. The DAG was reduced to show only the terms that are most relevant to glucose metabolism. The grey ellipses contain the genes that are annotated to the connected GO term and the colour of the GO terms indicates different levels of significance, as indicated by the legend.<p><b>Copyright information:</b></p><p>Taken from "MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters"</p><p>http://www.biomedcentral.com/1471-2164/9/105</p><p>BMC Genomics 2008;9():105-105.</p><p>Published online 28 Feb 2008</p><p>PMCID:PMC2277412.</p><p></p