AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast
AnGeLi: A Tool for the Analysis of Gene Lists from Fission Yeast
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DOI：
10.3389/fgene.2015.00330
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发表时间：
2015-11-16
影响因子：
3.7
通讯作者：
Baehler, Jureg
中科院分区：
文献类型：
--
作者：
Bitton, Danny A.;Schubert, Falk;Baehler, Jureg
全基因组测定和筛选通常会产生大量的基因或蛋白质。在这些列表中丰富功能或其他生物特性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是具有挑战性和耗时的，因为与查询基因列表进行比较的相关数据分布在许多不同的来源中。我们已经开发了AngeLi（基因列表分析），一个直观的，集成的网络工具，用于全面和定制的基因列表的询问，从裂殖酵母，裂殖酵母。AnGeLi在多个定性和定量信息源中寻找显著的丰富，包括基因和表型本体，遗传和蛋白质相互作用，基因，转录物，翻译和蛋白质的许多特征，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，半衰期，结构域和分子量等，以及共同调节或在突变时导致相同表型的不同基因组。AngeLi使用强大的统计数据，可以根据特定需求量身定制。它还提供了上传用户定义的基因集以与查询列表进行比较的选项。通过一个综合的数据提交表格，AngeLi鼓励社区贡献更多的策划基因列表，以进一步提高这一资源的有用性，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，可以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，通过该工具，S。pombe的研究人员可以从基因组数据中发现新的观点和意想不到的联系。AngeLi可在www.bahlerlab.info/AnGeLi免费获得。
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 .