Interactive exploration of integrated biological datasets using context-sensitive workflows.
Interactive exploration of integrated biological datasets using context-sensitive workflows.
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DOI：
10.3389/fgene.2014.00021
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发表时间：
2014
影响因子：
3.7
通讯作者：
Guthke R
中科院分区：
文献类型：
--
作者：
Horn F;Rittweger M;Taubert J;Lysenko A;Rawlings C;Guthke R
网络推理利用实验高通量数据重建分子相互作用网络，可以预测网络实体之间的新关系。尽管实验数据量不断增加，但每种建模技术的参数不能仅根据实验数据进行优化，而是需要定性评估所得网络的组件是否描述了实验设置。候选列表优先级排序和验证建立在数据集成和数据可视化的基础上。支持此过程的工具的应用仅限于探索较小的信息网络，因为大量信息的显示和解释在计算工作量和用户体验方面具有挑战性。 Ondex 软件框架通过可定制的上下文相关菜单进行了扩展，允许在交互式数据探索期间为选定的一组候选者提供额外的集成和数据分析选项。我们使用 InterProScan、PubMed Central 文献检索和基于序列的同源性检索提供实时数据集成的新功能。我们应用 Ondex 系统来整合构巢曲霉的公开数据并分析转录组数据。我们通过提出差异表达真菌基因簇特定基因的功能注释的新假设来证明我们的方法的优点。我们对 Ondex 框架的扩展使得克服数据集成和交互式分析之间的分离成为可能。更具体地说，可以在选定的子网络上执行计算要求较高的计算，而不会丢失整个网络的任何信息。此外，我们的扩展允许直接访问在线生物数据库，这有助于保持集成信息最新。
Network inference utilizes experimental high-throughput data for the reconstruction of molecular interaction networks where new relationships between the network entities can be predicted. Despite the increasing amount of experimental data, the parameters of each modeling technique cannot be optimized based on the experimental data alone, but needs to be qualitatively assessed if the components of the resulting network describe the experimental setting. Candidate list prioritization and validation builds upon data integration and data visualization. The application of tools supporting this procedure is limited to the exploration of smaller information networks because the display and interpretation of large amounts of information is challenging regarding the computational effort and the users' experience. The Ondex software framework was extended with customizable context-sensitive menus which allow additional integration and data analysis options for a selected set of candidates during interactive data exploration. We provide new functionalities for on-the-fly data integration using InterProScan, PubMed Central literature search, and sequence-based homology search. We applied the Ondex system to the integration of publicly available data for Aspergillus nidulans and analyzed transcriptome data. We demonstrate the advantages of our approach by proposing new hypotheses for the functional annotation of specific genes of differentially expressed fungal gene clusters. Our extension of the Ondex framework makes it possible to overcome the separation between data integration and interactive analysis. More specifically, computationally demanding calculations can be performed on selected sub-networks without losing any information from the whole network. Furthermore, our extensions allow for direct access to online biological databases which helps to keep the integrated information up-to-date.
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影响因子：
14.9
作者：
Kanehisa M;Goto S;Sato Y;Furumichi M;Tanabe M
通讯作者：
Tanabe M
影响因子：
14.9
作者：
Flicek P;Ahmed I;Amode MR;Barrell D;Beal K;Brent S;Carvalho-Silva D;Clapham P;Coates G;Fairley S;Fitzgerald S;Gil L;García-Girón C;Gordon L;Hourlier T;Hunt S;Juettemann T;Kähäri AK;Keenan S;Komorowska M;Kulesha E;Longden I;Maurel T;McLaren WM;Muffato M;Nag R;Overduin B;Pignatelli M;Pritchard B;Pritchard E;Riat HS;Ritchie GR;Ruffier M;Schuster M;Sheppard D;Sobral D;Taylor K;Thormann A;Trevanion S;White S;Wilder SP;Aken BL;Birney E;Cunningham F;Dunham I;Harrow J;Herrero J;Hubbard TJ;Johnson N;Kinsella R;Parker A;Spudich G;Yates A;Zadissa A;Searle SM
通讯作者：
Searle SM
影响因子：
1.9
作者：
Cockell, Simon J.;Weile, Jochen;Wipat, Anil
通讯作者：
Wipat, Anil
影响因子：
4.3
作者：
Huttenhower C;Hofmann O
通讯作者：
Hofmann O
影响因子：
14.9
作者：
Hull D;Wolstencroft K;Stevens R;Goble C;Pocock MR;Li P;Oinn T
通讯作者：
Oinn T