PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.
PlasmoDraft: a database of Plasmodium falciparum gene function predictions based on postgenomic data.
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DOI：
10.1186/1471-2105-9-440
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发表时间：
2008-10-16
影响因子：
3
通讯作者：
Gascuel O
中科院分区：
文献类型：
--
作者：
Bréhélin L;Dufayard JF;Gascuel O
恶性疟原虫是疟疾的主要病原体，在预测的5 484个蛋白质中，约60%与其他生物体中的蛋白质没有足够的序列相似性，以保证提供功能分配。因此，需要非同源性方法来获得这些未表征基因的功能线索。我们提出PlasmoDraft，一个基于后基因组数据的恶性疟原虫基因的基因本体论（GO）注释预测数据库。PlasmoDraft的预测是通过名为Gonna的Guilt By Association方法实现的。这涉及（1）一个预测器，它根据基因图谱（用转录组、蛋白质组或相互作用组数据测量）与GeneDB已经注释的基因的相似性为基因提出GO注释;（2）一个估计用每个数据源实现的预测的置信度的程序;（3）一个结合所有数据源以提供预测的全局总结和置信度估计的程序。Gonna已应用于所有恶性疟原虫基因，使用大多数公开可用的转录组，蛋白质组和相互作用组数据源。Gonna提供了许多基因的预测，没有任何注释。例如，在生物过程本体中没有任何注释的2434个基因与特定GO术语（例如Rosetting、抗原变异）相关联，并且在这些基因中，841个具有高于50%的置信度值。在细胞组分和分子功能本体中，分别有1905和1540个未表征的基因与特定的GO术语相关（740和329个置信度值高于50%）。所有预测沿着其置信度值都已在PlasmoDraft中编译，因此PlasmoDraft提供了可以使用这些数据源实现的GO注释预测的广泛数据库。数据库可以通过不同的方式访问。全局视图允许快速检查根据各种数据源以高置信度预测的GO项。基因视图和GO术语视图允许搜索附加到给定基因的潜在GO术语，以及潜在地属于给定GO术语的基因。
Of the 5 484 predicted proteins of Plasmodium falciparum, the main causative agent of malaria, about 60% do not have sufficient sequence similarity with proteins in other organisms to warrant provision of functional assignments. Non-homology methods are thus needed to obtain functional clues for these uncharacterized genes. We present PlasmoDraft , a database of Gene Ontology (GO) annotation predictions for P. falciparum genes based on postgenomic data. Predictions of PlasmoDraft are achieved with a Guilt By Association method named Gonna. This involves (1) a predictor that proposes GO annotations for a gene based on the similarity of its profile (measured with transcriptome, proteome or interactome data) with genes already annotated by GeneDB; (2) a procedure that estimates the confidence of the predictions achieved with each data source; (3) a procedure that combines all data sources to provide a global summary and confidence estimate of the predictions. Gonna has been applied to all P. falciparum genes using most publicly available transcriptome, proteome and interactome data sources. Gonna provides predictions for numerous genes without any annotations. For example, 2 434 genes without any annotations in the Biological Process ontology are associated with specific GO terms (e.g. Rosetting, Antigenic variation), and among these, 841 have confidence values above 50%. In the Cellular Component and Molecular Function ontologies, 1 905 and 1 540 uncharacterized genes are associated with specific GO terms, respectively (740 and 329 with confidence value above 50%). All predictions along with their confidence values have been compiled in PlasmoDraft, which thus provides an extensive database of GO annotation predictions that can be achieved with these data sources. The database can be accessed in different ways. A global view allows for a quick inspection of the GO terms that are predicted with high confidence, depending on the various data sources. A gene view and a GO term view allow for the search of potential GO terms attached to a given gene, and genes that potentially belong to a given GO term.
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DOI：
10.1073/pnas.97.1.262
发表时间：
2000-01-04
影响因子：
11.1
作者：
Brown, MPS;Grundy, WN;Haussler, D
通讯作者：
Haussler, D
影响因子：
9.8
作者：
Bozdech, Zbynek;Llinas, Manuel;Pulliam, Brian Lee;Wong, Edith D;Zhu, Jingchun;DeRisi, Joseph L
通讯作者：
DeRisi, Joseph L
影响因子：
12.3
作者：
Shock JL;Fischer KF;DeRisi JL
通讯作者：
DeRisi JL
影响因子：
4.9
作者：
Dahl, Erica L.;Shock, Jennifer L.;Rosenthal, Philip J.
通讯作者：
Rosenthal, Philip J.
影响因子：
14.9
作者：
Chen, Y;Xu, D
通讯作者：
Xu, D