An interactive tool for visualization of relationships between gene expression profiles

BACKGROUND: Application of phenetic methods to gene expression analysis proved to be a successful approach. Visualizing the results in a 3-dimentional space may further enhance these techniques. RESULTS: We designed and built TreeBuilder3D, an interactive viewer for visualizing the hierarchical relationships between expression profiles such as SAGE libraries or microarrays. The program allows loading expression data as plain text files and visualizing the relative differences of the analyzed datasets in 3-dimensional space using various distance metrics. CONCLUSION: TreeBuilder3D provides a simple interface and has a small size. Written in Java, TreeBuilder3D is a platform-independent, open source application, which may be useful in analysis of large-scale gene expression data

Deep SAGE analysis of the Caenorhabditis elegans transcriptome

We employed the Tag-seq technique to generate global transcription profiles for different strains and life stages of the nematode C. elegans. Tag-seq generates cDNA tags as does Serial Analysis of Gene Expression (SAGE), but the method yields a much larger number of tags, generating much larger data sets than SAGE. We examined differences in the performance of SAGE and Tag-seq by comparing gene expression data for 13 pairs of libraries. We identified genes for which expression was consistently changed in long-lived worms. Additional genes emerged in the deeper Tag-seq profiles, including several ‘signature’ genes found among those zup-regulated in long-lived dauer larvae (cki-1, aak-2 and daf-16). Fifty to sixty percent of the genes differentially expressed in daf-2(−) versus daf-2(+) adults had fragmentary or no functional annotation, suggesting the involvement of as yet unstudied pathways in aging. We were able to distinguish between changes in gene expression associated with altered genotype or altered growth conditions. We found 62 cases of possible mRNA isoform switching in the 13 Tag-seq libraries, whereas the 13 SAGE libraries allowed detection of only 15 such occurrences. We observed strong expression of anti-sense transcripts for several mitochondrial genes, but nuclear anti-sense transcripts were neither abundant nor consistently expressed among the libraries

The modENCODE Data Coordination Center: lessons in harvesting comprehensive experimental details.

The model organism Encyclopedia of DNA Elements (modENCODE) project is a National Human Genome Research Institute (NHGRI) initiative designed to characterize the genomes of Drosophila melanogaster and Caenorhabditis elegans. A Data Coordination Center (DCC) was created to collect, store and catalog modENCODE data. An effective DCC must gather, organize and provide all primary, interpreted and analyzed data, and ensure the community is supplied with the knowledge of the experimental conditions, protocols and verification checks used to generate each primary data set. We present here the design principles of the modENCODE DCC, and describe the ramifications of collecting thorough and deep metadata for describing experiments, including the use of a wiki for capturing protocol and reagent information, and the BIR-TAB specification for linking biological samples to experimental results. modENCODE data can be found at http://www.modencode.org

modMine: flexible access to modENCODE data.

In an effort to comprehensively characterize the functional elements within the genomes of the important model organisms Drosophila melanogaster and Caenorhabditis elegans, the NHGRI model organism Encyclopaedia of DNA Elements (modENCODE) consortium has generated an enormous library of genomic data along with detailed, structured information on all aspects of the experiments. The modMine database (http://intermine.modencode.org) described here has been built by the modENCODE Data Coordination Center to allow the broader research community to (i) search for and download data sets of interest among the thousands generated by modENCODE; (ii) access the data in an integrated form together with non-modENCODE data sets; and (iii) facilitate fine-grained analysis of the above data. The sophisticated search features are possible because of the collection of extensive experimental metadata by the consortium. Interfaces are provided to allow both biologists and bioinformaticians to exploit these rich modENCODE data sets now available via modMine

An interactive tool for visualization of relationships between gene expression profiles-0

<p><b>Copyright information:</b></p><p>Taken from "An interactive tool for visualization of relationships between gene expression profiles"</p><p>BMC Bioinformatics 2006;7():193-193.</p><p>Published online 6 Apr 2006</p><p>PMCID:PMC1456991.</p><p>Copyright © 2006 Ruzanov and Jones; licensee BioMed Central Ltd.</p>iption", which may provide the application with information about total number of tags in a library and an alternative description (different from id string). The description becomes visible when user checks "Descr" box on the control panel. : data in GEO format. Highlighted are the fields, which are used for identification of the data-source and normalization of the tag counts. Also, it is possible to derive the short description from the field "Sample_title", which is analogous to the generic "Description" field

Discovery of novel alternatively spliced C. elegans transcripts by computational analysis of SAGE data

Background: Alternative RNA splicing allows cells to produce multiple protein isoforms from one gene. These isoforms may have specialized functions, and may be tissue- or stage-specific. Our aim was to use computational analysis of SAGE and genomic data to predict alternatively spliced transcripts expressed in C. elegans. Results We predicted novel alternatively spliced variants and confirmed five of eighteen candidates selected for experimental validation by RT-PCR tests and DNA sequencing. Conclusion We show that SAGE data can be efficiently used to discover alternative mRNA isoforms, including those with skipped exons or retained introns. Our results also imply that C. elegans may produce a larger number of alternatively spliced transcripts than initially estimated.Other UBCNon UBCReviewedFacult

Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data-0

<p><b>Copyright information:</b></p><p>Taken from "Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data"</p><p>http://www.biomedcentral.com/1471-2164/8/447</p><p>BMC Genomics 2007;8():447-447.</p><p>Published online 30 Nov 2007</p><p>PMCID:PMC2216036.</p><p></p>ice junctions as shown. Introns and flanking 13 bp sequences were used for extraction of SAGE tags identifying cases of intron retention. For exon skipping validation, one of the primers spanned the predicted splice junction, so that hybridization with the template mRNA was possible only if the predicted transcript was present in the mRNA pool. Detection of an RT-PCR product with a larger size than expected for a normally spliced isoform confirmed intron retention events

Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data-1

<p><b>Copyright information:</b></p><p>Taken from "Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data"</p><p>http://www.biomedcentral.com/1471-2164/8/447</p><p>BMC Genomics 2007;8():447-447.</p><p>Published online 30 Nov 2007</p><p>PMCID:PMC2216036.</p><p></p>nes 1–8 correspond to the genes C33G3.4, C52E4.6a, F27D4.4, T01G5.1, T05B4.1, T14G10.1, W04G5.9 and Y49F6B.8. PCR products of the expected sizes (400 – 600 bp) were observed for four genes. *DNA sequencing did not confirm one of the candidates (C33G3.4, lane 1 on the left panel). : the results of the intron retention analysis. The positions of the PCR product for normally spliced isoforms (empty arrows) and isoforms with intron retention (black arrows) are shown. Lanes 1–10 correspond to the genes B0041.3, C08B6.13, C14C6.5, C24G6.3, D1054.10, F07C6.2, R09E10.3, T23G7.5, W01A8.3 and Y116A8C.30. * Additional RT-PCR experiments with oligo(dT) primer followed by DNA sequencing disproved three candidates (C08B6.13, R09E10.3 and W01A8.3)

Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data-2

<p><b>Copyright information:</b></p><p>Taken from "Discovery of novel alternatively spliced transcripts by computational analysis of SAGE data"</p><p>http://www.biomedcentral.com/1471-2164/8/447</p><p>BMC Genomics 2007;8():447-447.</p><p>Published online 30 Nov 2007</p><p>PMCID:PMC2216036.</p><p></p>ice junctions as shown. Introns and flanking 13 bp sequences were used for extraction of SAGE tags identifying cases of intron retention. For exon skipping validation, one of the primers spanned the predicted splice junction, so that hybridization with the template mRNA was possible only if the predicted transcript was present in the mRNA pool. Detection of an RT-PCR product with a larger size than expected for a normally spliced isoform confirmed intron retention events