Cargando…
BEST: a web server for brain expression Spatio-temporal pattern analysis
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, multi...
Autores principales: | , , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896511/ https://www.ncbi.nlm.nih.gov/pubmed/31805847 http://dx.doi.org/10.1186/s12859-019-3222-6 |
_version_ | 1783476794081411072 |
---|---|
author | Guo, Liyuan Lin, Wei Zhang, Yidan Li, Wenhan Wang, Jing |
author_facet | Guo, Liyuan Lin, Wei Zhang, Yidan Li, Wenhan Wang, Jing |
author_sort | Guo, Liyuan |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-6896511 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-68965112019-12-11 BEST: a web server for brain expression Spatio-temporal pattern analysis Guo, Liyuan Lin, Wei Zhang, Yidan Li, Wenhan Wang, Jing BMC Bioinformatics Software 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. BioMed Central 2019-12-05 /pmc/articles/PMC6896511/ /pubmed/31805847 http://dx.doi.org/10.1186/s12859-019-3222-6 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Software Guo, Liyuan Lin, Wei Zhang, Yidan Li, Wenhan Wang, Jing BEST: a web server for brain expression Spatio-temporal pattern analysis |
title | 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_short | BEST: a web server for brain expression Spatio-temporal pattern analysis |
title_sort | best: a web server for brain expression spatio-temporal pattern analysis |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6896511/ https://www.ncbi.nlm.nih.gov/pubmed/31805847 http://dx.doi.org/10.1186/s12859-019-3222-6 |
work_keys_str_mv | AT guoliyuan bestawebserverforbrainexpressionspatiotemporalpatternanalysis AT linwei bestawebserverforbrainexpressionspatiotemporalpatternanalysis AT zhangyidan bestawebserverforbrainexpressionspatiotemporalpatternanalysis AT liwenhan bestawebserverforbrainexpressionspatiotemporalpatternanalysis AT wangjing bestawebserverforbrainexpressionspatiotemporalpatternanalysis |