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Expression profiling of the schizont and trophozoite stages of Plasmodium falciparum with a long-oligonucleotide microarray.

Genome biology | Mar 6, 2003

BACKGROUND: The worldwide persistence of drug-resistant Plasmodium falciparum, the most lethal variety of human malaria, is a global health concern. The P. falciparum sequencing project has brought new opportunities for identifying molecular targets for antimalarial drug and vaccine development. RESULTS: We developed a software package, ArrayOligoSelector, to design an open reading frame (ORF)-specific DNA microarray using the publicly available P. falciparum genome sequence. Each gene was represented by one or more long 70 mer oligonucleotides selected on the basis of uniqueness within the genome, exclusion of low-complexity sequence, balanced base composition and proximity to the 3' end. A first-generation microarray representing approximately 6,000 ORFs of the P. falciparum genome was constructed. Array performance was evaluated through the use of control oligonucleotide sets with increasing levels of introduced mutations, as well as traditional northern blotting. Using this array, we extensively characterized the gene-expression profile of the intraerythrocytic trophozoite and schizont stages of P. falciparum. The results revealed extensive transcriptional regulation of genes specialized for processes specific to these two stages. CONCLUSIONS: DNA microarrays based on long oligonucleotides are powerful tools for the functional annotation and exploration of the P. falciparum genome. Expression profiling of trophozoites and schizonts revealed genes associated with stage-specific processes and may serve as the basis for future drug targets and vaccine development.

Pubmed ID: 12620119 RIS Download

Mesh terms: Animals | Blotting, Northern | Gene Expression Profiling | Oligonucleotide Array Sequence Analysis | Plasmodium falciparum | RNA, Protozoan

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Fungal Databases

This website contains a list of five fungal genome databases from The J. Craig Venter Institute. Aspergillus genomes: -Aspergillus fumigatus (strain-Af 293) -Aspergillus clavatus -Neosartorya fischeri Other Fungal Genomes: -Cryptococcus neoformans (strain-JEC21) -Coccidioides posadasii

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Pompep

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ApiDB PlasmoDB

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. It brings together data provided by numerous laboratories worldwide (see the Data Sources page), and adds its own data analysis. PlasmoDB is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB Bioinformatics Resource Center (BRC) umbrella. PlasmoDB contains numerous data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis. Organisms * Annotated genomes: Plasmodium falciparum, Plasmodium vivax, Plasmodium yoelii, Plasmodium berghei, Plasmodium chabaudi, Plasmodium knowlesi * Unannotated genomes: Plasmodium reichenowi, Plasmodium gallinaceum * Others: environmental isolate sequences from numerous species PlasmoDB provides programmatic access to its searches, via REST Web Services.

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ArrayOligoSelector

Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene.

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