 ResearchGenome-wide gene expression in response to parasitoid attack in DrosophilaBregje Wertheim1,2 1 Centre for Evolutionary Genomics, Department of Biology, University College London, Darwin Building, Gower Street, London WC1E 6BT, UK 2 NERC Centre for Population Biology, Division of Biology, Imperial College London, Silwood Park Campus, Ascot, Berkshire SL5 7PY, UK 3 European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK 4 Huffington Center on Aging and Molecular and Human Genetics, Baylor College of Medicine, One Baylor Plaza, Houston, TX 77030, USA 5 Department of Entomology, 420 Biological Sciences, University of Georgia, Athens, GA 30602-2603, USA
Genome Biology 2005, 6:R94doi:10.1186/gb-2005-6-11-r94
Subject areas: Immunology, Microbiology and parasitology Additional filesAdditional data file 1: Annotation of probe sets with significantly different expression profiles in parasitized and control larvae. The annotation includes a matching score describing the fraction of the 14 probes that matched perfectly to the annotated transcript sequence, the gene name(s) assigned to probe sets, and functional and structural annotations for each gene. Whenever more than one gene was assigned to a probe set, an asterisk indicates which annotation was used in the EASE analysis. Format: PDF Size: 1.3MB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 2: Expression profile and upstream motifs of all genes per cluster. The log2 expression values at the time points (hours) after parasitoid attack are shown for all replicates (blue circles for the control larvae; red triangles for the parasitized larvae) and the lines denote the average expression at each time point. The strength of match for the putative regulatory motifs in the upstream sequences is indicated by the height of the bars. Format: PDF Size: 4.5MB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 3: A full list of putative regulatory motifs that were significantly over-represented in our clusters of genes. Motifs were identified by MotifRegressor and over-representation was calculated in Clover. The Representative Motifs denote the degenerate motifs, using IUPAC Ambiguous DNA Characters. The Raw Score measures the strength of match and the frequency of occurrence. Significance (denoted in the last two columns) is based on the comparison with the upstream sequences of 1,000 randomly chosen genes represented on the Affymetrix Drosophila 1 Genome Array, respectively - all genes on Drosophila chromosome 2. Format: PDF Size: 89KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 4: A diagrammatic representation of the degenerate motifs of the putative TFBMs. The size of the letters represents the likelihood of its occurrence at each position in the sequence. Format: PDF Size: 100KB Download file This file can be viewed with: Adobe Acrobat Reader Additional data file 5: Normalized data of the probe sets with significantly differential expression profiles in parasitized and control larvae. The expression values (log2 transformed) for the five biologic replicates at each of nine time points after parasitism are provided for the paired sets of parasitized and control larvae. Format: TXT Size: 171KB Download file |
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