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PhenUMA：一种整合基因与疾病之间生物医学关系的工具。

PhenUMA: a tool for integrating the biomedical relationships among genes and diseases.

作者信息

Rodríguez-López Rocío, Reyes-Palomares Armando, Sánchez-Jiménez Francisca, Medina Miguel Ángel

机构信息

Departamento de Biología Molecular y Bioquímica, Universidad de Málaga, Andalucía Tech, Facultad de Ciencias, and IBIMA (Biomedical Research Institute of Málaga), Málaga, Spain.

CIBER de Enfermedades Raras (CIBERER), E-29071, Málaga, Spain.

出版信息

BMC Bioinformatics. 2014 Nov 25;15(1):375. doi: 10.1186/s12859-014-0375-1.

DOI:10.1186/s12859-014-0375-1
PMID:25420641
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC4260198/
Abstract

BACKGROUND

Several types of genetic interactions in humans can be directly or indirectly associated with the causal effects of mutations. These interactions are usually based on their co-associations to biological processes, coexistence in cellular locations, coexpression in cell lines, physical interactions and so on. In addition, pathological processes can present similar phenotypes that have mutations either in the same genomic location or in different genomic regions. Therefore, integrative resources for all of these complex interactions can help us prioritize the relationships between genes and diseases that are most deserving to be studied by researchers and physicians.

RESULTS

PhenUMA is a web application that displays biological networks using information from biomedical and biomolecular data repositories. One of its most innovative features is to combine the benefits of semantic similarity methods with the information taken from databases of genetic diseases and biological interactions. More specifically, this tool is useful in studying novel pathological relationships between functionally related genes, merging diseases into clusters that share specific phenotypes or finding diseases related to reported phenotypes.

CONCLUSIONS

This framework builds, analyzes and visualizes networks based on both functional and phenotypic relationships. The integration of this information helps in the discovery of alternative pathological roles of genes, biological functions and diseases. PhenUMA represents an advancement toward the use of new technologies for genomics and personalized medicine.

摘要

背景

人类中的几种基因相互作用可直接或间接与突变的因果效应相关。这些相互作用通常基于它们与生物过程的共关联、在细胞位置的共存、在细胞系中的共表达、物理相互作用等。此外，病理过程可呈现相似的表型，这些表型在相同基因组位置或不同基因组区域发生突变。因此，整合所有这些复杂相互作用的资源可帮助我们确定研究人员和医生最值得研究的基因与疾病之间的关系的优先级。

结果

PhenUMA是一个网络应用程序，它利用生物医学和生物分子数据存储库中的信息显示生物网络。其最具创新性的功能之一是将语义相似性方法的优势与从遗传疾病和生物相互作用数据库中获取的信息相结合。更具体地说，该工具在研究功能相关基因之间的新型病理关系、将疾病合并为共享特定表型的簇或发现与报道表型相关的疾病方面很有用。

结论

该框架基于功能和表型关系构建、分析和可视化网络。这些信息的整合有助于发现基因、生物学功能和疾病的替代病理作用。PhenUMA代表了在将新技术用于基因组学和个性化医学方面的一项进展。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/f82b2ccd49a6/12859_2014_375_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/0a130f003392/12859_2014_375_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/f50ae08a138c/12859_2014_375_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/591268552334/12859_2014_375_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/16b6cea63172/12859_2014_375_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/41d9940919fb/12859_2014_375_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/f82b2ccd49a6/12859_2014_375_Fig6_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/0a130f003392/12859_2014_375_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/f50ae08a138c/12859_2014_375_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/591268552334/12859_2014_375_Fig3_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/16b6cea63172/12859_2014_375_Fig4_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/41d9940919fb/12859_2014_375_Fig5_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3761/4260198/f82b2ccd49a6/12859_2014_375_Fig6_HTML.jpg

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