BEST: a web server for brain expression Spatio-temporal pattern analysis
Abstract Background Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from genetics studies. By using reference data from brain expression studie...
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doaj-3ffb78c7b65e41678ff0ef0df24bce4f2020-12-06T12:56:53ZengBMCBMC Bioinformatics1471-21052019-12-012011810.1186/s12859-019-3222-6BEST: a web server for brain expression Spatio-temporal pattern analysisLiyuan Guo0Wei Lin1Yidan Zhang2Wenhan Li3Jing Wang4CAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of SciencesCAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of SciencesCAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of SciencesOumeng V medical LaboratoryCAS Key Laboratory of Mental Health, Institute of Psychology, Chinese Academy of SciencesAbstract Background Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from genetics studies. By using reference data from brain expression studies, multiple types of comprehensive gene expression pattern analysis have been performed on psychiatric genetic results. These systems-level spatial-temporal expression pattern analyses provided evidence on specific brain regions, developmental stages and molecular pathways that are possibly involved in psychiatric pathophysiology. At present, there is no online tool for such systematic analysis, which hinders the applications of analysis by non-informatics researchers such as experimental biologists and clinical molecular biologists. Results We developed the BEST web server to support Brain Expression Spatio-Temporal pattern analysis. There are three highlighted features of BEST: 1) visualization: it generates user-friendly visual results that are easy to interpret, including heatmaps, Venn diagrams, gene co-expression networks and cluster-based Manhattan gene plots; these results illustrate the complex spatio-temporal expression patterns, including expression quantification and correlation between genes; 2) integration: it provides comprehensive human brain spatio-temporal expression patterns by integrating data from currently available databases; 3) multi-dimensionality: it analyses input genes as both a whole set and several subsets (clusters) which are enriched according to co-expression patterns, and it also presents the correlation between genetic and expression data. Conclusions To the best of our knowledge, BEST is the first data tool to support comprehensive human brain spatial-temporal expression pattern analysis. It helps to bridge disease-related genetic studies and mechanism studies, provides clues for key gene and molecular system identification, and supports the analysis of disease sensitive brain region and age stages. BEST is freely available at http://best.psych.ac.cn .https://doi.org/10.1186/s12859-019-3222-6Web serverBrain expression pattern analysisSpatio-temporalCo-expression clusterVisualization |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Liyuan Guo Wei Lin Yidan Zhang Wenhan Li Jing Wang |
spellingShingle |
Liyuan Guo Wei Lin Yidan Zhang Wenhan Li Jing Wang BEST: a web server for brain expression Spatio-temporal pattern analysis BMC Bioinformatics Web server Brain expression pattern analysis Spatio-temporal Co-expression cluster Visualization |
author_facet |
Liyuan Guo Wei Lin Yidan Zhang Wenhan Li Jing Wang |
author_sort |
Liyuan Guo |
title |
BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_short |
BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_full |
BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_fullStr |
BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_full_unstemmed |
BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_sort |
best: a web server for brain expression spatio-temporal pattern analysis |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-12-01 |
description |
Abstract Background Dysregulated gene expression patterns have been reported in several mental disorders. Limited by the difficulty of obtaining samples, psychiatric molecular mechanism research still relies heavily on clues from genetics studies. By using reference data from brain expression studies, multiple types of comprehensive gene expression pattern analysis have been performed on psychiatric genetic results. These systems-level spatial-temporal expression pattern analyses provided evidence on specific brain regions, developmental stages and molecular pathways that are possibly involved in psychiatric pathophysiology. At present, there is no online tool for such systematic analysis, which hinders the applications of analysis by non-informatics researchers such as experimental biologists and clinical molecular biologists. Results We developed the BEST web server to support Brain Expression Spatio-Temporal pattern analysis. There are three highlighted features of BEST: 1) visualization: it generates user-friendly visual results that are easy to interpret, including heatmaps, Venn diagrams, gene co-expression networks and cluster-based Manhattan gene plots; these results illustrate the complex spatio-temporal expression patterns, including expression quantification and correlation between genes; 2) integration: it provides comprehensive human brain spatio-temporal expression patterns by integrating data from currently available databases; 3) multi-dimensionality: it analyses input genes as both a whole set and several subsets (clusters) which are enriched according to co-expression patterns, and it also presents the correlation between genetic and expression data. Conclusions To the best of our knowledge, BEST is the first data tool to support comprehensive human brain spatial-temporal expression pattern analysis. It helps to bridge disease-related genetic studies and mechanism studies, provides clues for key gene and molecular system identification, and supports the analysis of disease sensitive brain region and age stages. BEST is freely available at http://best.psych.ac.cn . |
topic |
Web server Brain expression pattern analysis Spatio-temporal Co-expression cluster Visualization |
url |
https://doi.org/10.1186/s12859-019-3222-6 |
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