DFLAT: functional annotation for human development.
DFLAT: functional annotation for human development.
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DOI：
10.1186/1471-2105-15-45
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发表时间：
2014-02-07
影响因子：
3
通讯作者：
Slonim DK
中科院分区：
文献类型：
--
作者：
Wick HC;Drabkin H;Ngu H;Sackman M;Fournier C;Haggett J;Blake JA;Bianchi DW;Slonim DK
最近对人类胎儿和新生儿发育的基因组研究增加，导致需要广泛表征基因在不同发育阶段的功能作用。基因本体（Gene Ontology， GO）是一种有价值且被广泛使用的表征基因功能的资源，可能是最适合用于此目的的功能注释系统。然而，部分由于研究人类分子遗传效应的困难，即使是目前收集的人类基因和基因产物的全面GO注释，对于希望研究人类胎儿基因功能的科学家来说，也往往缺乏足够的发育背景。塔夫茨发育功能注释（DFLAT）项目旨在通过使用人工和半自动GO程序管理人类胎儿基因功能，提高胎儿基因表达和调控分析的质量。合格的注释随后被贡献到GO数据库中，并包含在GO发布的人类数据中。DFLAT已经产生了大量的功能注释，我们证明这些注释提供了有关发育基因组学的有价值的信息。通过将现有的GO注释与13344个新的DFLAT注释相结合，可以收集基因集（涉及相同功能或生物过程的基因），用于新的分析。对几个数据集的表达进行了基因集分析，包括21和18三体胎儿的羊水RNA、脐带血和支气管肺发育不良新生儿的血液，在有和没有DFLAT注释的情况下进行了分析。使用DFLAT注释对表达数据进行功能分析增加了涉及基因集的数量，反映了DFLAT对当前知识的改进表示。盲法文献综述支持DFLAT注释获得的新重要发现的有效性。新牵连的重要基因组也为未来的研究提出了具体的假设。总的来说，DFLAT项目提供了新的功能注释和基因集，有可能提高我们解释人类胎儿和新生儿发育基因组研究的能力。
Recent increases in genomic studies of the developing human fetus and neonate have led to a need for widespread characterization of the functional roles of genes at different developmental stages. The Gene Ontology (GO), a valuable and widely-used resource for characterizing gene function, offers perhaps the most suitable functional annotation system for this purpose. However, due in part to the difficulty of studying molecular genetic effects in humans, even the current collection of comprehensive GO annotations for human genes and gene products often lacks adequate developmental context for scientists wishing to study gene function in the human fetus. The Developmental FunctionaL Annotation at Tufts (DFLAT) project aims to improve the quality of analyses of fetal gene expression and regulation by curating human fetal gene functions using both manual and semi-automated GO procedures. Eligible annotations are then contributed to the GO database and included in GO releases of human data. DFLAT has produced a considerable body of functional annotation that we demonstrate provides valuable information about developmental genomics. A collection of gene sets (genes implicated in the same function or biological process), made by combining existing GO annotations with the 13,344 new DFLAT annotations, is available for use in novel analyses. Gene set analyses of expression in several data sets, including amniotic fluid RNA from fetuses with trisomies 21 and 18, umbilical cord blood, and blood from newborns with bronchopulmonary dysplasia, were conducted both with and without the DFLAT annotation. Functional analysis of expression data using the DFLAT annotation increases the number of implicated gene sets, reflecting the DFLAT’s improved representation of current knowledge. Blinded literature review supports the validity of newly significant findings obtained with the DFLAT annotations. Newly implicated significant gene sets also suggest specific hypotheses for future research. Overall, the DFLAT project contributes new functional annotation and gene sets likely to enhance our ability to interpret genomic studies of human fetal and neonatal development.
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基因本体论：2011年的增强。
影响因子：
14.9
作者：
Gene Ontology Consortium
通讯作者：
Gene Ontology Consortium
影响因子：
7.1
作者：
Ashoor, G.;Syngelaki, A.;Nicolaides, K. H.
通讯作者：
Nicolaides, K. H.
DOI：
10.1073/pnas.0511150103
发表时间：
2006-02-28
影响因子：
11.1
作者：
Bourquin, JP;Subramanian, A;Orkin, SH
通讯作者：
Orkin, SH
影响因子：
7.2
作者：
Bianchi, Diana W.;Platt, Lawrence D.;Rava, Richard P.
通讯作者：
Rava, Richard P.
影响因子：
5.8
作者：
Goeman, Jelle J.;Mansmann, Ulrich
通讯作者：
Mansmann, Ulrich