RESUMO
Identifying sets of genes that are specifically expressed in certain tissues or in response to an environmental stimulus is useful for designing reporter constructs, generating gene expression markers, or for understanding gene regulatory networks. We have developed an easy-to-use online tool for defining a desired expression profile (a modification of our Expression Angler program), which can then be used to identify genes exhibiting patterns of expression that match this profile as closely as possible. Further, we have developed another online tool, Cistome, for predicting or exploring cis-elements in the promoters of sets of co-expressed genes identified by such a method, or by other methods. We present two use cases for these tools, which are freely available on the Bio-Analytic Resource at http://BAR.utoronto.ca.
Assuntos
Arabidopsis/metabolismo , Mineração de Dados , Arabidopsis/genética , Bases de Dados Genéticas , Regulação da Expressão Gênica de Plantas/genética , Regulação da Expressão Gênica de Plantas/fisiologia , Regiões Promotoras Genéticas/genética , SoftwareRESUMO
Large numbers of sequences are now readily available for many plant species, allowing easy identification of homologous genes. However, orthologous gene identification across multiple species is made difficult by evolutionary events such as whole-genome or segmental duplications. Several developmental atlases of gene expression have been produced in the past couple of years, and it may be possible to use these transcript abundance data to refine ortholog predictions. In this study, clusters of homologous genes between seven plant species - Arabidopsis, soybean, Medicago truncatula, poplar, barley, maize and rice - were identified. Following this, a pipeline to rank homologs within gene clusters by both sequence and expression profile similarity was devised by determining equivalent tissues between species, with the best expression profile match being termed the 'expressolog'. Five electronic fluorescent pictograph (eFP) browsers were produced as part of this effort, to aid in visualization of gene expression data and to complement existing eFP browsers at the Bio-Array Resource (BAR). Within the eFP browser framework, these expression profile similarity rankings were incorporated into an Expressolog Tree Viewer to allow cross-species homolog browsing by both sequence and expression pattern similarity. Global analyses showed that orthologs with the highest sequence similarity do not necessarily exhibit the highest expression pattern similarity. Other orthologs may show different expression patterns, indicating that such genes may require re-annotation or more specific annotation. Ultimately, it is envisaged that this pipeline will aid in improvement of the functional annotation of genes and translational plant research.
Assuntos
Armazenamento e Recuperação da Informação , Magnoliopsida/genética , Homologia de Sequência , Software , Transcriptoma , Arabidopsis/genética , Bases de Dados Genéticas , Flores/genética , Perfilação da Expressão Gênica , Regulação da Expressão Gênica de Plantas , Hordeum/genética , Internet , Medicago truncatula/genética , Família Multigênica , Especificidade de Órgãos , Oryza/genética , Folhas de Planta/genética , Raízes de Plantas/genética , Populus/genética , Glycine max/genética , Xilema/genética , Zea mays/genéticaRESUMO
Next-generation genomic sequencing technologies have made it possible to directly map mutations responsible for phenotypes of interest via direct sequencing. However, most mapping strategies proposed to date require some prior genetic analysis, which can be very time-consuming even in genetically tractable organisms. Here we present a de novo method for rapidly and robustly mapping the physical location of EMS mutations by sequencing a small pooled F2 population. This method, called Next Generation Mapping (NGM), uses a chastity statistic to quantify the relative contribution of the parental mutant and mapping lines to each SNP in the pooled F2 population. It then uses this information to objectively localize the candidate mutation based on its exclusive segregation with the mutant parental line. A user-friendly, web-based tool for performing NGM analysis is available at http://bar.utoronto.ca/NGM. We used NGM to identify three genes involved in cell-wall biology in Arabidopsis thaliana, and, in a power analysis, demonstrate success in test mappings using as few as ten F2 lines and a single channel of Illumina Genome Analyzer data. This strategy can easily be applied to other model organisms, and we expect that it will also have utility in crops and any other eukaryote with a completed genome sequence.
Assuntos
Arabidopsis/genética , Mapeamento Cromossômico/métodos , Metanossulfonato de Etila/farmacologia , Sequenciamento de Nucleotídeos em Larga Escala/métodos , Mutação/genética , Arabidopsis/efeitos dos fármacos , Sequência de Bases , Parede Celular/genética , DNA de Plantas/química , DNA de Plantas/genética , Genômica , Internet , Mutação/efeitos dos fármacos , Fenótipo , Polimorfismo de Nucleotídeo Único , Plântula/genética , Análise de Sequência de DNARESUMO
Transcutaneous electrical nerve stimulation (TENS) has been used to treat chronic pain syndromes and has been reported to be of some utility in the treatment of postsurgical pain. A randomized, blinded, placebo-controlled trial was designed to evaluate the utility of TENS after total knee arthroplasty. Patients were randomly enrolled into patient-controlled anesthesia (PCA) alone, PCA plus TENS, or PCA plus sham TENS. The cumulative dose of morphine by PCA for each group was used as the end-point of the study. There was no significant reduction in the requirement for patient-controlled analgesia with or without TENS. We conclude that there is no utility for TENS in the postoperative management of pain after knee arthroplasty.