PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
PhenoLink--a web-tool for linking phenotype to ~omics data for bacteria: application to gene-trait matching for Lactobacillus plantarum strains.
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DOI：
10.1186/1471-2164-13-170
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发表时间：
2012-05-04
期刊：
影响因子：
4.4
通讯作者：
van Hijum SA
中科院分区：
文献类型：
--
作者：
Bayjanov JR;Molenaar D;Tzeneva V;Siezen RJ;van Hijum SA
将表型与组学技术产生的高通量分子生物学信息联系起来，可以揭示生物体表型背后的细胞机制。 ~组学数据集通常非常大且嘈杂，具有许多特征（例如基因、代谢物丰度）。因此，将表型与组学数据相关联需要一种对噪声具有鲁棒性并且可以处理大型且多样化的数据集的方法。我们开发了一个网络工具 PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/)，它使用成熟的新技术将表型与组学数据集链接起来。 PhenoLink 估算缺失值并预处理输入数据 (i) 以减少数据中的固有噪声，以及 (ii) 平衡随机森林算法的缺陷，而特征（例如基因）选择正是基于该算法。预处理的数据用于特征（例如基因）选择，以识别与表型的关系。我们应用 PhenoLink 根据 42 种植物乳杆菌菌株中 2847 个基因的存在/缺失以及这些菌株在多种实验条件（包括糖生长和二氧化氮产生）下的表型测量来识别基因-表型关系。根据基因的重要性（预测值）对基因进行排序，以正确预测给定菌株的表型。除了已知的基因与表型关系之外，我们还发现了新的关系。 PhenoLink 是一种易于访问的网络工具，有助于从大型且通常嘈杂的表型和组学数据集中识别关系。 PhenoLink 中提供的表型链接的可视化允许对链接进行优先级排序、查找特征之间的关系、查找表型之间的关系以及识别表型数据中的异常值。 PhenoLink 可用于揭示与大量组学数据的表型联系，例如基因存在/不存在（通过 CGH 或下一代测序确定）、基因表达（通过微阵列或 RNA-seq 等确定）或代谢物丰度（通过 GC-MS 等确定）。
Linking phenotypes to high-throughput molecular biology information generated by ~omics technologies allows revealing cellular mechanisms underlying an organism's phenotype. ~Omics datasets are often very large and noisy with many features (e.g., genes, metabolite abundances). Thus, associating phenotypes to ~omics data requires an approach that is robust to noise and can handle large and diverse data sets. We developed a web-tool PhenoLink (http://bamics2.cmbi.ru.nl/websoftware/phenolink/) that links phenotype to ~omics data sets using well-established as well new techniques. PhenoLink imputes missing values and preprocesses input data (i) to decrease inherent noise in the data and (ii) to counterbalance pitfalls of the Random Forest algorithm, on which feature (e.g., gene) selection is based. Preprocessed data is used in feature (e.g., gene) selection to identify relations to phenotypes. We applied PhenoLink to identify gene-phenotype relations based on the presence/absence of 2847 genes in 42 Lactobacillus plantarum strains and phenotypic measurements of these strains in several experimental conditions, including growth on sugars and nitrogen-dioxide production. Genes were ranked based on their importance (predictive value) to correctly predict the phenotype of a given strain. In addition to known gene to phenotype relations we also found novel relations. PhenoLink is an easily accessible web-tool to facilitate identifying relations from large and often noisy phenotype and ~omics datasets. Visualization of links to phenotypes offered in PhenoLink allows prioritizing links, finding relations between features, finding relations between phenotypes, and identifying outliers in phenotype data. PhenoLink can be used to uncover phenotype links to a multitude of ~omics data, e.g., gene presence/absence (determined by e.g.: CGH or next-generation sequencing), gene expression (determined by e.g.: microarrays or RNA-seq), or metabolite abundance (determined by e.g.: GC-MS).
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影响因子：
14.9
作者：
Klimke W;Agarwala R;Badretdin A;Chetvernin S;Ciufo S;Fedorov B;Kiryutin B;O'Neill K;Resch W;Resenchuk S;Schafer S;Tolstoy I;Tatusova T
通讯作者：
Tatusova T
DOI：
10.1093/bioinformatics/btq381
发表时间：
2010-09-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Van Landeghem S;Abeel T;Saeys Y;Van de Peer Y
通讯作者：
Van de Peer Y
DOI：
10.1073/pnas.0702377104
发表时间：
2007-08-28
影响因子：
11.1
作者：
Morand, Brigitte;Muehlemann, Kathrin
通讯作者：
Muehlemann, Kathrin
影响因子：
3
作者：
Blagus R;Lusa L
通讯作者：
Lusa L
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y