RESUMEN
BACKGROUND: During the last decade, a great number of extremely valuable large-scale genomics and proteomics datasets have become available to the research community. In addition, dropping costs for conducting high-throughput sequencing experiments and the option to outsource them considerably contribute to an increasing number of researchers becoming active in this field. Even though various computational approaches have been developed to analyze these data, it is still a laborious task involving prudent integration of many heterogeneous and frequently updated data sources, creating a barrier for interested scientists to accomplish their own analysis. RESULTS: We have implemented Dintor, a data integration framework that provides a set of over 30 tools to assist researchers in the exploration of genomics and proteomics datasets. Each of the tools solves a particular task and several tools can be combined into data processing pipelines. Dintor covers a wide range of frequently required functionalities, from gene identifier conversions and orthology mappings to functional annotation of proteins and genetic variants up to candidate gene prioritization and Gene Ontology-based gene set enrichment analysis. Since the tools operate on constantly changing datasets, we provide a mechanism to unambiguously link tools with different versions of archived datasets, which guarantees reproducible results for future tool invocations. We demonstrate a selection of Dintor's capabilities by analyzing datasets from four representative publications. The open source software can be downloaded and installed on a local Unix machine. For reasons of data privacy it can be configured to retrieve local data only. In addition, the Dintor tools are available on our public Galaxy web service at http://dintor.eurac.edu . CONCLUSIONS: Dintor is a computational annotation framework for the analysis of genomic and proteomic datasets, providing a rich set of tools that cover the most frequently encountered tasks. A major advantage is its capability to consistently handle multiple versions of tool-associated datasets, supporting the researcher in delivering reproducible results.
Asunto(s)
Curaduría de Datos/métodos , Genómica/métodos , Proteómica/métodos , Bases de Datos Genéticas , Programas InformáticosRESUMEN
Cardiac myxomas are the most common primary cardiac tumors. Surgical resection usually provides definitive treatment; however, postoperative tumor recurrence has been reported, especially when myxomas occur as part of a familial pattern. Only a few cases of 2nd recurrence of nonfamilial cardiac myxoma have been reported. We report 2 cases of nonfamilial cardiac myxoma, with multiple recurrences after surgical resection. The possibility of repeated recurrence of cardiac myxomas demonstrates the importance of regular echocardiography after surgical resection in order to detect such recurrence. Future studies, including genetic analysis of patients with recurrent cardiac myxomas, are warranted to investigate the nature of these tumors.
Asunto(s)
Procedimientos Quirúrgicos Cardíacos , Neoplasias Cardíacas/cirugía , Mixoma/cirugía , Recurrencia Local de Neoplasia/cirugía , Adulto , Anciano , Femenino , Neoplasias Cardíacas/diagnóstico por imagen , Humanos , Masculino , Mixoma/diagnóstico por imagen , Recurrencia Local de Neoplasia/diagnóstico por imagen , Resultado del Tratamiento , UltrasonografíaRESUMEN
Stimulation of the Drosophila immune response activates NF-kappaB and JNK signaling pathways. For example, infection by Gram-negative bacteria induces the Imd signaling pathway, leading to the activation of the NF-kappaB-like transcription factor Relish and the expression of a battery of genes encoding antimicrobial peptides. Bacterial infection also activates the JNK pathway, but the role of this pathway in the immune response has not yet been established. Genetic experiments suggest that the Drosophila homolog of the mammalian MAPK kinase kinase, TAK1 (transforming growth factor beta-activated kinase 1), activates both the JNK and NF-kappaB pathways following immune stimulation. In this report, we demonstrate that Drosophila TAK1 functions as both the Drosophila IkappaB kinase-activating kinase and the JNK kinase-activating kinase. However, we found that JNK signaling is not required for antimicrobial peptide gene expression but is required for the activation of other immune inducible genes, including Punch, sulfated, and malvolio. Thus, JNK signaling appears to play an important role in the cellular immune response and the stress response.