Bitton Danny A, Schubert Falk, Dey Shoumit, Okoniewski Michal, Smith Graeme C, Khadayate Sanjay, Pancaldi Vera, Wood Valerie, Bähler Jürg
Research Department of Genetics, Evolution and Environment - UCL Genetics Institute, University College London London, UK.
Scientific IT Services, ETH Zürich Zürich, Switzerland.
Front Genet. 2015 Nov 16;6:330. doi: 10.3389/fgene.2015.00330. eCollection 2015.
Genome-wide assays and screens typically result in large lists of genes or proteins. Enrichments of functional or other biological properties within such lists can provide valuable insights and testable hypotheses. To systematically detect these enrichments can be challenging and time-consuming, because relevant data to compare against query gene lists are spread over many different sources. We have developed AnGeLi (Analysis of Gene Lists), an intuitive, integrated web-tool for comprehensive and customized interrogation of gene lists from the fission yeast, Schizosaccharomyces pombe. AnGeLi searches for significant enrichments among multiple qualitative and quantitative information sources, including gene and phenotype ontologies, genetic and protein interactions, numerous features of genes, transcripts, translation, and proteins such as copy numbers, chromosomal positions, genetic diversity, RNA polymerase II and ribosome occupancy, localization, conservation, half-lives, domains, and molecular weight among others, as well as diverse sets of genes that are co-regulated or lead to the same phenotypes when mutated. AnGeLi uses robust statistics which can be tailored to specific needs. It also provides the option to upload user-defined gene sets to compare against the query list. Through an integrated data submission form, AnGeLi encourages the community to contribute additional curated gene lists to further increase the usefulness of this resource and to get the most from the ever increasing large-scale experiments. AnGeLi offers a rigorous yet flexible statistical analysis platform for rich insights into functional enrichments and biological context for query gene lists, thus providing a powerful exploratory tool through which S. pombe researchers can uncover fresh perspectives and unexpected connections from genomic data. AnGeLi is freely available at: www.bahlerlab.info/AnGeLi.
全基因组分析和筛选通常会产生大量的基因或蛋白质列表。这些列表中功能或其他生物学特性的富集可以提供有价值的见解和可检验的假设。系统地检测这些富集可能具有挑战性且耗时，因为与查询基因列表进行比较的相关数据分散在许多不同的来源中。我们开发了AnGeLi（基因列表分析），这是一个直观的集成网络工具，用于全面和定制地查询来自裂殖酵母粟酒裂殖酵母的基因列表。AnGeLi在多个定性和定量信息源中搜索显著富集，包括基因和表型本体、遗传和蛋白质相互作用、基因、转录本、翻译和蛋白质的众多特征，如拷贝数、染色体位置、遗传多样性、RNA聚合酶II和核糖体占有率、定位、保守性、半衰期、结构域和分子量等，以及在突变时共同调控或导致相同表型的不同基因集。AnGeLi使用强大的统计方法，可以根据特定需求进行定制。它还提供上传用户定义基因集以与查询列表进行比较的选项。通过集成的数据提交表单，AnGeLi鼓励社区贡献更多经过整理的基因列表，以进一步提高该资源的实用性，并从不断增加的大规模实验中获得最大收益。AnGeLi提供了一个严谨而灵活的统计分析平台，用于深入了解查询基因列表的功能富集和生物学背景，从而提供了一个强大的探索工具，粟酒裂殖酵母研究人员可以通过该工具从基因组数据中发现新的观点和意想不到的联系。AnGeLi可在以下网址免费获取：www.bahlerlab.info/AnGeLi。
