SeaBase：一个用于基因网络推断的多物种转录组资源与平台。

SeaBase: a multispecies transcriptomic resource and platform for gene network inference.

作者信息

Fischer Antje H L, Mozzherin Dmitry, Eren A Murat, Lans Kristen D, Wilson Nathan, Cosentino Carlo, Smith Joel

机构信息

*Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy*Marine Biological Laboratory, Woods Hole, MA 02543, USA; Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138, USA; Systems & Control Engineering, University of Magna Graecia, 88100 Catanzaro, Italy

出版信息

Integr Comp Biol. 2014 Jul;54(2):250-63. doi: 10.1093/icb/icu065. Epub 2014 Jun 6.

DOI:10.1093/icb/icu065

PMID:24907201

Abstract

Marine and aquatic animals are extraordinarily useful as models for identifying mechanisms of development and evolution, regeneration, resistance to cancer, longevity and symbiosis, among many other areas of research. This is due to the great diversity of these organisms and their wide-ranging capabilities. Genomics tools are essential for taking advantage of these "free lessons" of nature. However, genomics and transcriptomics are challenging in emerging model systems. Here, we present SeaBase, a tool for helping to meet these needs. Specifically, SeaBase provides a platform for sharing and searching transcriptome data. More importantly, SeaBase will support a growing number of tools for inferring gene network mechanisms. The first dataset available on SeaBase is a developmental transcriptomic profile of the sea anemone Nematostella vectensis (Anthozoa, Cnidaria). Additional datasets are currently being prepared and we are aiming to expand SeaBase to include user-supplied data for any number of marine and aquatic organisms, thereby supporting many potentially new models for gene network studies. SeaBase can be accessed online at: http://seabase.core.cli.mbl.edu.

摘要

海洋和水生动物作为研究发育与进化、再生、抗癌、长寿及共生等众多领域机制的模型，具有极高的价值。这得益于这些生物的多样性及其广泛的能力。基因组学工具对于利用这些大自然的“免费课程”至关重要。然而，在新兴模型系统中，基因组学和转录组学面临挑战。在此，我们展示SeaBase，这是一款有助于满足这些需求的工具。具体而言，SeaBase提供了一个用于共享和搜索转录组数据的平台。更重要的是，SeaBase将支持越来越多用于推断基因网络机制的工具。SeaBase上的首个数据集是海葵星状海葵（刺胞动物门，珊瑚纲）的发育转录组图谱。目前正在准备其他数据集，我们旨在扩展SeaBase，以纳入用户提供的任意数量海洋和水生生物的数据，从而支持许多潜在的基因网络研究新模型。可通过以下网址在线访问SeaBase：http://seabase.core.cli.mbl.edu 。