Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data.
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DOI：
10.1186/1471-2105-12-282
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发表时间：
2011-07-12
影响因子：
3
通讯作者：
Pellegrini M
中科院分区：
文献类型：
--
作者：
Lopez D;Casero D;Cokus SJ;Merchant SS;Pellegrini M
基因组测序的进展正在以指数级的速度进行，每年都有几个新的藻类基因组可用。该社区面临的挑战之一是将基因组中编码的蛋白质序列与生物功能联系起来。虽然大多数基因组组装项目为预测的蛋白质序列生成注释，但它们通常是有限的，并整合了有限数量的数据库中的功能术语。另一个挑战是使用注释来解释由基因组规模的数据集产生的大量“有趣的”基因列表。以前，这些基因列表必须在几个独立的生物数据库中进行分析，通常是在逐个基因的基础上。相比之下，几个注释数据库，如David，集成了来自多个功能数据库的数据，并揭示了大型基因列表的潜在生物学主题。虽然已经为动物建立了几个这样的数据库，但目前还没有一个数据库可用于藻类的研究。由于人们对藻类作为生物燃料潜在来源的新兴趣，以及多种藻类基因组序列的出现，出现了对这样一个数据库的重大需求，以处理日益增长的藻类基因组数据概要。藻类功能注释工具是一个基于Web的综合分析套件，集成了来自多个途径、本体和蛋白质家族数据库的注释数据。目前的版本提供了对模式藻莱茵衣藻的注释，未来将包括更多的基因组。该网站允许用户通过识别相关的功能术语及其丰富来解释大型基因列表。此外，对几个实验条件的表达数据进行了汇编和分析，以提供基于表达的丰富搜索。还提供了一种基于跨越这些条件的基因表达来搜索功能相关基因的工具。其他功能包括在KEGG路径图上动态显示基因和批量基因识别符转换。藻类功能注释工具旨在通过将来自多个注释数据库的数据合并到一个集中工具中，为藻类基因组学提供一个综合的数据挖掘环境。该网站旨在加快功能注释和基因列表的解释过程，例如那些来自高通量RNA-SEQ实验的列表。该工具在http://pathways.mcdb.ucla.edu.上公开提供
Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion. The Algal Functional Annotation Tool aims to provide an integrated data-mining environment for algal genomics by combining data from multiple annotation databases into a centralized tool. This site is designed to expedite the process of functional annotation and the interpretation of gene lists, such as those derived from high-throughput RNA-seq experiments. The tool is publicly available at http://pathways.mcdb.ucla.edu.
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影响因子：
14.9
作者：
Caspi R;Altman T;Dale JM;Dreher K;Fulcher CA;Gilham F;Kaipa P;Karthikeyan AS;Kothari A;Krummenacker M;Latendresse M;Mueller LA;Paley S;Popescu L;Pujar A;Shearer AG;Zhang P;Karp PD
通讯作者：
Karp PD
影响因子：
11.6
作者：
Rochaix, JD
通讯作者：
Rochaix, JD
影响因子：
14.9
作者：
Finn RD;Mistry J;Tate J;Coggill P;Heger A;Pollington JE;Gavin OL;Gunasekaran P;Ceric G;Forslund K;Holm L;Sonnhammer EL;Eddy SR;Bateman A
通讯作者：
Bateman A
影响因子：
7.4
作者：
Miller, Rachel;Wu, Guangxi;Benning, Christoph
通讯作者：
Benning, Christoph
影响因子：
14.9
作者：
Huang, Da Wei;Sherman, Brad T.;Lempicki, Richard A.
通讯作者：
Lempicki, Richard A.